Error in re-building vignettes:
  ...
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/

Please cite the 'censReg' package as:
Henningsen, Arne (2017). censReg: Censored Regression (Tobit) Models. R package version 0.5. http://CRAN.R-Project.org/package=censReg.

If you have questions, suggestions, or comments regarding the 'censReg' package, please use a forum or 'tracker' at the R-Forge site of the 'sampleSelection' project:
https://r-forge.r-project.org/projects/sampleselection/

Error: processing vignette ‘censReg.Rnw’ failed with diagnostics:
 chunk 3 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘ggrepel’
Error in re-building vignettes:
  ...
Quitting from lines 63-74 (Census2016.Rmd) 
Error: processing vignette ‘Census2016.Rmd’ failed with diagnostics:
object ‘.CensusDataTables’ not found
Execution halted
Package required but not available: ‘ggmap’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘dplyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘alr3’
Packages required but not available:
  ‘car’ ‘dplyr’ ‘ggplot2’ ‘ggrepel’ ‘tibble’

Package suggested but not available for checking: ‘productplots’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘systemfit’ ‘cplm’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘nonlinearTseries’
Packages required but not available: ‘rgl’ ‘ggplot2’ ‘sphereplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘tibble’
Running examples in ‘checkmate-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: checkTibble
> ### Title: Check if an argument is a tibble
> ### Aliases: checkTibble check_tibble assertTibble assert_tibble testTibble
> ###   test_tibble expect_tibble
> 
> ### ** Examples
> 
> library(tibble)
Error in library(tibble) : there is no package called ‘tibble’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 160-170 (checkmate.Rmd) 
Error: processing vignette ‘checkmate.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘pROC’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘seriation’ ‘rgl’ ‘speaq’
Running examples in ‘ChemoSpec-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hmapSpectra
> ### Title: Seriated Heat Map for a Spectra Object
> ### Aliases: hmapSpectra
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 
> data(SrE.IR)
> # Let's look just at the carbonyl region
> IR <- removeFreq(SrE.IR, rem.freq = SrE.IR$freq > 1850 | SrE.IR$freq < 1650)
> res <- hmapSpectra(IR, col = heat.colors(5), labCol = FALSE)
Error in hmapSpectra(IR, col = heat.colors(5), labCol = FALSE) : 
  You need to install package seriation to use this function
Execution halted
Packages required but not available: ‘dbplyr’ ‘dplyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘tibble’ ‘purrr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘drc’ ‘qpcR’ ‘RDML’
Error in re-building vignettes:
  ...
Quitting from lines 13-46 (unstacking.bars.Rmd) 
Error: processing vignette ‘unstacking.bars.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘Hmisc’ ‘ggplot2’ ‘dplyr’ ‘ggmap’ ‘tigris’

Package suggested but not available for checking: ‘choroplethrAdmin1’

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

Packages suggested but not available for checking: ‘ggplot2’ ‘stm’

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

Package suggested but not available for checking: ‘dbplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 21-92 (cifti_work.Rmd) 
Error: processing vignette ‘cifti_work.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Packages required but not available:
  ‘FactoMineR’ ‘factoextra’ ‘GGally’ ‘dendextend’ ‘viridis’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘userfriendlyscience’
Package suggested but not available for checking: ‘dendextend’
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(factors = "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
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages required but not available: ‘dplyr’ ‘tibble’

Packages suggested but not available for checking: ‘broom’ ‘tidyverse’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘dbplyr’ ‘feather’ ‘ggplot2’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘qualtRics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readxl’
Packages required but not available: ‘ggplot2’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readtext’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cld2)
  > 
  > test_check("cld2")
  ── 1. Error: vectorised input works (@test-detect.R#5)  ────────────────────────
  there is no package called 'readtext'
  1: library(readtext) at testthat/test-detect.R:5
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: vectorised input works (@test-detect.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘dplyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rstan’ ‘ggplot2’

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

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

Packages suggested but not available for checking: ‘tensorflow’ ‘keras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘clubSandwich-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vcovCR.ivreg
> ### Title: Cluster-robust variance-covariance matrix for an ivreg object.
> ### Aliases: vcovCR.ivreg
> 
> ### ** Examples
> 
> library(AER)
Error in library(AER) : there is no package called ‘AER’
Execution halted
Running ‘testthat.R’ [183s/247s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clubSandwich)
  Registered S3 method overwritten by 'clubSandwich':
    method    from    
    bread.mlm sandwich
  > set.seed(20171124)
  > test_check("clubSandwich")
  ── 1. Error: (unknown) (@test_ivreg.R#3)  ──────────────────────────────────────
  there is no package called 'AER'
  1: library(AER, quietly = TRUE) at testthat/test_ivreg.R:3
  2: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test_plm-first-differences.R#5)  ──────────────────────
  there is no package called 'AER'
  1: data(Fatalities, package = "AER") at testthat/test_plm-first-differences.R:5
  2: find.package(package, lib.loc, verbose = verbose)
  3: stop(gettextf("there is no package called %s", sQuote(pkg)), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 593 SKIPPED: 5 FAILED: 2
  1. Error: (unknown) (@test_ivreg.R#3) 
  2. Error: (unknown) (@test_plm-first-differences.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘Hmisc’ ‘extracat’

Package suggested but not available for checking: ‘dendextend’

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.
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 37-42 (using-clusternomics.Rmd) 
Error: processing vignette ‘using-clusternomics.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘car’ ‘data.tree’ ‘dendextend’ ‘tibble’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘quanteda’ ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GGally’ ‘dplyr’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggraph’ ‘dplyr’ ‘ggplot2’ ‘viridis’ ‘tidygraph’ ‘ggrepel’

Package suggested but not available for checking: ‘Seurat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘smoof’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forcats’ ‘tidyr’ ‘purrr’ ‘dplyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggstance’

Packages suggested but not available for checking: ‘WeightIt’ ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘likert’ ‘dplyr’ ‘tidyr’ ‘skimr’ ‘DT’ ‘haven’ ‘readr’
  ‘mice’ ‘tibble’ ‘purrr’ ‘rio’

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

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘car’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 19-30 (codingMatrices.Rnw) 
Error: processing vignette ‘codingMatrices.Rnw’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 108-110 (Temporal_Diversity_Indices.Rmd) 
Error: processing vignette ‘Temporal_Diversity_Indices.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘useful’ ‘dplyr’ ‘tibble’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘haplo.stats’

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

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rgl’

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: ‘dplyr’ ‘purrr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘plotly’

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

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

Package suggested but not available for checking: ‘DT’

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

Packages suggested but not available for checking: ‘inSilicoDb’ ‘GEOmetadb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘comperes’ ‘dplyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘tidyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘compositions-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arrows3D
> ### Title: arrows in 3D, based on package rgl
> ### Aliases: arrows3D arrows3D.default
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> x <- cbind(rnorm(10),rnorm(10),rnorm(10))
> plot3D(x)
Loading required namespace: rgl
Failed with error:  ‘there is no package called ‘rgl’’
Loading required namespace: rgl
Failed with error:  ‘there is no package called ‘rgl’’
Error in loadNamespace(name) : there is no package called ‘rgl’
Calls: plot3D ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package required but not available: ‘purrr’

Packages suggested but not available for checking: ‘ggplot2’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘dplyr’ ‘tidyselect’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘hdrcde’ ‘DendSer’
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’ ‘tibble’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘miceadds’

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

Package suggested but not available for checking: ‘alphahull’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘contoureR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contourLinesR
> ### Title: Get Contour Lines (list)
> ### Aliases: contourLinesR
> 
> ### ** Examples
> 
> library(contoureR)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘rms’ ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rstan’ ‘ggplot2’

Package suggested but not available for checking: ‘bayesplot’

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

Package suggested but not available for checking: ‘car’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tCorpus$top_features
> ### Title: Show top features
> ### Aliases: tCorpus$top_features top_features
> 
> ### ** Examples
> 
> tc = tokens_to_tcorpus(corenlp_tokens, token_id_col = 'id')
> 
> tc$top_features('lemma')
Error in loadNamespace(name) : there is no package called ‘reshape2’
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package required but not available: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘missMDA’
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘seriation’ ‘purrr’ ‘tibble’ ‘ggrepel’

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: ‘cosinor’ ‘ggplot2’ ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dataRetrieval’ ‘dplyr’ ‘ggplot2’ ‘tidyr’

Package suggested but not available for checking: ‘hurricaneexposure’

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

Packages suggested but not available for checking:
  ‘choroplethr’ ‘ggplot2’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggmap’ ‘ggplot2’ ‘purrr’ ‘rnoaa’ ‘tibble’ ‘tidyr’ ‘tigris’

Package suggested but not available for checking: ‘countytimezones’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘vdiffr’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rms’ ‘dplyr’ ‘tidyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qvalue’
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘rgl’ ‘tibble’ ‘tidyr’

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

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

Packages suggested but not available for checking:
  ‘ggplot2’ ‘tidyr’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘UpSetR’ ‘dplyr’ ‘ggplot2’ ‘ggridges’ ‘tidyr’ ‘purrr’
  ‘clusterProfiler’

Packages suggested but not available for checking: ‘dbplyr’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rcrossref’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggmcmc’

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: ‘tables’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘haven’ ‘labelled’ ‘readr’ ‘readxl’ ‘tibble’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘tidytext’ ‘tibble’

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.
Package suggested but not available for checking: ‘haven’
Packages required but not available: ‘ggplot2’ ‘qte’

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

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 38-45 (csp.Rmd) 
Error: processing vignette ‘csp.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘readr’
Package suggested but not available for checking: ‘crawl’
Error in re-building vignettes:
  ...
Quitting from lines 36-71 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Running examples in ‘CTM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CDTM
> ### Title: Document Term Matrix
> ### Aliases: CDTM
> 
> ### ** Examples
> 
> library(CTM)
> a1 <- "hello taiwan"
> b1 <- "world of tank"
> c1 <- "taiwan weather"
> d1 <- "local weather"
> text1 <- t(data.frame(a1,b1,c1,d1))
> dtm1 <- CTDM(doc = text1, weighting = "tfidf",EngTermDeleted = FALSE, shortTermDeleted = FALSE)
Error in unzip(file.path(jiebapath, "dict", "jieba.dict.zip"), exdir = file.path(jiebapath,  : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/jieba.dict.utf8': Read-only file system
Error in unzip(file.path(jiebapath, "dict", "hmm_model.zip"), exdir = file.path(jiebapath,  : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/hmm_model.utf8': Read-only file system
Error in unzip(file.path(jiebapath, "dict", "idf.zip"), exdir = file.path(jiebapath,  : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/idf.utf8': Read-only file system
2018-06-25 15:49:34 ../inst/include/lib/DictTrie.hpp:159 FATAL exp: [ifs.is_open()] false. open /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/jieba.dict.utf8 failed.
terminate called after throwing an instance of 'Rcpp::exception'
  what():  2018-06-25 15:49:34 ../inst/include/lib/DictTrie.hpp:159 FATAL exp: [ifs.is_open()] false. open /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/jieba.dict.utf8 failed.
Aborted
Package required but not available: ‘tea’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 12-17 (cubist.Rmd) 
Error: processing vignette ‘cubist.Rmd’ failed with diagnostics:
there is no package called 'caret'
Execution halted
Packages required but not available: ‘feature’ ‘hdrcde’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘purrr’ ‘tibble’ ‘ggplot2’

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 suggested but not available for checking:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘ggbeeswarm’
Error in re-building vignettes:
  ...
Quitting from lines 110-118 (how_to_test_CVs.Rmd) 
Error: processing vignette ‘how_to_test_CVs.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘cvxclustr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cvxclust
> ### Title: Convex Clustering Path via Variable Splitting Methods
> ### Aliases: cvxclust
> 
> ### ** Examples
> 
> ## Clusterpaths for Mammal Dentition
> data(mammals)
> X <- as.matrix(mammals[,-1])
> X <- t(scale(X,center=TRUE,scale=FALSE))
> n <- ncol(X)
> 
> ## Pick some weights and a sequence of regularization parameters.
> k <- 5
> phi <- 0.5
> w <- kernel_weights(X,phi)
> w <- knn_weights(w,k,n)
> gamma <- seq(0.0,43, length.out=100)
> 
> ## Perform clustering
> sol <- cvxclust(X,w,gamma)
Warning in cvxclust_ama(X, Lambda, ix - 1, M1 - 1, M2 - 1, s1, s2, w[w >  :
  The stepsize nu may be too large. Setting it to maximum of 1/n and 1/AnM.
> 
> ## Plot the cluster path
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package suggested but not available for checking: ‘leaflet’
Error in re-building vignettes:
  ...
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'
Execution halted
Package required but not available: ‘ggplot2’

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’ ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking: ‘dbplyr’ ‘readr’

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.
Packages required but not available: ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘purrr’

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

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

Package suggested but not available for checking: ‘d3r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘pdp’ ‘ggplot2’ ‘breakDown’ ‘factorMerger’ ‘ggpubr’

Package suggested but not available for checking: ‘dplyr’

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

Packages suggested but not available for checking: ‘ggplot2’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: dams
Loading required package: ggplot2
Loading required package: maps
Loading required package: mapproj
Quitting from lines 67-71 (dams.Rmd) 
Error: processing vignette ‘dams.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Packages required but not available:
  ‘adegenet’ ‘tidyr’ ‘ggplot2’ ‘rgl’ ‘pca3d’ ‘pegas’ ‘SNPassoc’
  ‘StAMPP’ ‘qvalue’ ‘plotly’

Packages suggested but not available for checking: ‘mmod’ ‘PopGenReport’

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

Packages suggested but not available for checking:
  ‘DataVisualizations’ ‘AdaptGauss’ ‘rgl’ ‘ProjectionBasedClustering’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘nycflights13’ ‘tibble’
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’ ‘tibble’

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

Package suggested but not available for checking: ‘Rhipe’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 50-72 (get_started.Rmd) 
Error: processing vignette ‘get_started.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘readr’ ‘tibble’

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

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kableExtra’
Error in re-building vignettes:
  ...
Loading required package: lubridate

Attaching package: 'lubridate'

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

    date

Loading required package: stringr
Loading required package: Matrix
Loading required package: progress
dataPreparation 0.3.6
Type dataPrepNews() to see new features/changes/bug fixes.

Attaching package: 'data.table'

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

    hour, isoweek, mday, minute, month, quarter, second, wday,
    week, yday, year

Quitting from lines 16-54 (dataPreparation.Rmd) 
Error: processing vignette ‘dataPreparation.Rmd’ failed with diagnostics:
there is no package called 'kableExtra'
Execution halted
Packages suggested but not available for checking:
  ‘car’ ‘doBy’ ‘ggplot2’ ‘colormap’

VignetteBuilder packages required for checking but not installed:
  ‘car’ ‘doBy’ ‘ggplot2’ ‘colormap’

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

Package suggested but not available for checking: ‘treemap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘AdaptGauss’ ‘ggplot2’

Packages suggested but not available for checking:
  ‘plotly’ ‘ggmap’ ‘rgl’ ‘choroplethr’ ‘dplyr’

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

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SASxport’
Packages required but not available: ‘dplyr’ ‘tibble’

Package suggested but not available for checking: ‘nycflights13’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘seqHMM’ ‘TraMineR’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘purrr’

Packages suggested but not available for checking: ‘dbplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyselect’

Packages suggested but not available for checking: ‘Lahman’ ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readr’

Package suggested but not available for checking: ‘ggExtra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘DT’ ‘tidyr’
Error in re-building vignettes:
  ...
Quitting from lines 49-59 (RC_units.Rmd) 
Error: processing vignette ‘RC_units.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘PSF’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘cowplot’ ‘ggplot2’
Package required but not available: ‘Deducer’

Package suggested but not available for checking: ‘rgl’

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’ ‘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: ‘ggplot2’ ‘car’

Package suggested but not available for checking: ‘Hmisc’

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

Depends: includes the non-default packages:
  ‘JavaGD’ ‘Deducer’ ‘sp’ ‘maptools’ ‘OpenStreetMap’ ‘scales’ ‘rgdal’
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: ‘tibble’ ‘purrr’

Package suggested but not available for checking: ‘dplyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 115-125 (ODE_parameter_inference.Rmd) 
Error: processing vignette ‘ODE_parameter_inference.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘DiagrammeR’
Packages required but not available: ‘forecast’ ‘ftsa’ ‘rainbow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

Packages suggested but not available for checking:
  ‘seriation’ ‘heatmaply’ ‘d3heatmap’ ‘DendSer’

Packages which this enhances but not available for checking:
  ‘ggdendro’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘seriation’ ‘gapmap’
Error in re-building vignettes:
  ...
Quitting from lines 27-32 (example_figures.Rmd) 
Error: processing vignette ‘example_figures.Rmd’ failed with diagnostics:
there is no package called 'seriation'
Execution halted
Packages required but not available: ‘ggplot2’ ‘drc’

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

Package suggested but not available for checking: ‘missMDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘rgl’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘forcats’ ‘ggplot2’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘haven’ ‘readr’ ‘readxl’ ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘ijtiff’ ‘autothresholdr’ ‘filesstrings’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dexter’ ‘DT’ ‘dplyr’ ‘tidyr’ ‘tibble’ ‘readxl’ ‘readODS’ ‘ggplot2’
  ‘ggExtra’ ‘ggridges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyr’ ‘tibble’ ‘DT’ ‘purrr’ ‘dplyr’ ‘dbplyr’

Package suggested but not available for checking: ‘ggplot2’

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

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

Packages suggested but not available for checking:
  ‘ggplot2’ ‘MEGENA’ ‘cowplot’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘DiceDesign-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rss3d
> ### Title: 3D graphical tool for defect detection of Space-Filling Designs.
> ### Aliases: rss3d
> ### Keywords: design
> 
> ### ** Examples
> 
> 	# An orthogonal array in 3D   
> data(OA131)
> 
> 	# centering the design points of this 7-levels design
> OA <- (OA131 + 0.5)/7
> 
> 	# 2D projections onto coordinate axis 
> pairs(OA, xlim=c(0,1), ylim=c(0,1))
> 	# Now let us look at the 3D properties with the 3D RSS (requires the rgl package)
> rss <- rss3d(OA, lower=c(0,0,0), upper=c(1,1,1))

3D Radial Scanning Statistic (RSS) with GREENWOOD statistic
Discretization step (in degree) : 3

Maximum of RS statistic values (global statistic) per triplet of dimensions
(1,2,3) 0.2621302

[1] "Error : the package rgl is not installed"
Error in rss3d(OA, lower = c(0, 0, 0), upper = c(1, 1, 1)) : 
  object 'dir.max' not found
Execution halted
Package suggested but not available for checking: ‘GPareto’
Packages required but not available:
  ‘caret’ ‘dplyr’ ‘ggplot2’ ‘Hmisc’ ‘klaR’ ‘NMF’ ‘purrr’ ‘quantable’
  ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘dielectric-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AgPalik
> ### Title: AgPalik
> ### Aliases: AgPalik
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(AgPalik)
> str(AgPalik$raw())
'data.frame':	241 obs. of  4 variables:
 $ wavelength: num  0.155 0.207 0.248 0.275 0.31 ...
 $ epsilon   : cplx  1+0i 1+0i 1+0i ...
 $ real      : num  1 1 1 1 1.01 ...
 $ imag      : num  5.84e-06 1.68e-05 3.04e-05 4.42e-05 7.16e-05 ...
> AgPalik$comment
$source
[1] "Silver in the visible, Palik"

$units
[1] "nanometres"

> demo(AgPalik)


	demo(AgPalik)
	---- ~~~~~~~

> library(dielectric)

> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Calls: demo -> source -> withVisible -> eval -> eval -> library
Execution halted
Package required but not available: ‘tibble’

Packages suggested but not available for checking: ‘purrr’ ‘dplyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘diffrprojects’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package required but not available: ‘systemfit’

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

Packages suggested but not available for checking:
  ‘DiffusionRgqd’ ‘DiffusionRjgqd’

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

Package suggested but not available for checking: ‘DiffusionRgqd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘rgl’ ‘tidyr’
Running examples in ‘dimRed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_R_NX
> ### Title: plot_R_NX
> ### Aliases: plot_R_NX
> 
> ### ** Examples
> 
> 
> ## define which methods to apply
> embed_methods <- c("Isomap", "PCA")
> ## load test data set
> data_set <- loadDataSet("3D S Curve", n = 1000)
> ## apply dimensionality reduction
> data_emb <- lapply(embed_methods, function(x) embed(data_set, x))
2018-06-25 17:19:05: Isomap START
2018-06-25 17:19:05: constructing knn graph
2018-06-25 17:19:05: calculating geodesic distances
2018-06-25 17:19:07: cmdscale
2018-06-25 17:19:09: post processing
> names(data_emb) <- embed_methods
> ## plot the R_NX curves:
> plot_R_NX(data_emb) +
+     ggplot2::theme(legend.title = ggplot2::element_blank(),
+                    legend.position = c(0.5, 0.1),
+                    legend.justification = c(0.5, 0.1))
Error in chckpkg("ggplot2") : 
  require 'ggplot2' package, install it using install.packages('ggplot2')
Calls: plot_R_NX -> chckpkg
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 12-17 (DirectEffects.Rmd) 
Error: processing vignette ‘DirectEffects.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘alphahull’ ‘dplyr’
Running ‘ggplot.R’ [0s/1s]
  Running ‘lasso.R’ [0s/1s]
Running the tests in ‘tests/lasso.R’ failed.
Complete output:
  > library(directlabels)
  > data(prostate,package="ElemStatLearn")
  > pros <- subset(prostate,select=-train,train==TRUE)
  > ycol <- which(names(pros)=="lpsa")
  > x <- as.matrix(pros[-ycol])
  > y <- pros[[ycol]]
  > library(lars)
  Loaded lars 1.2
  
  > fit <- lars(x,y,type="lasso")
  > beta <- scale(coef(fit),FALSE,1/fit$normx)
  > 
  > ## Degenerate case: one 0 curves.
  > beta[, "gleason"] <- 0
  > arclength <- rowSums(abs(beta))
  > path <- data.frame(
  +   step=as.integer(row(beta)),
  +   variable=colnames(beta)[as.integer(col(beta))],
  +   arclength=arclength[as.integer(row(beta))],
  +   standardized.coef=as.numeric(beta))
  > library(ggplot2)
  Error in library(ggplot2) : there is no package called 'ggplot2'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘tidyr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggdendro’ ‘seriation’
Package suggested but not available for checking: ‘FactoMineR’
Packages suggested but not available for checking: ‘caret’ ‘pec’
Running examples in ‘discSurv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aucUno
> ### Title: Area under the Curve Estimation
> ### Aliases: aucUno
> ### Keywords: survival
> 
> ### ** Examples
> 
> #####################################################
> # Example with cross validation and unemployment data 
> 
> library(Ecdat)
Loading required package: Ecfun

Attaching package: ‘Ecfun’

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

    sign


Attaching package: ‘Ecdat’

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

    Orange

> library(caret)
Error in library(caret) : there is no package called ‘caret’
Execution halted
Running ‘UnitTestsDiscSurvDataTransform.R’ [3s/4s]
  Running ‘UnitTestsDiscSurvEstimation.R’ [2s/3s]
  Running ‘UnitTestsDiscSurvEvalShort.R’ [4s/5s]
  Running ‘UnitTestsDiscSurvEvaluation.R’ [2s/3s]
Running the tests in ‘tests/UnitTestsDiscSurvEvaluation.R’ failed.
Complete output:
  > library(discSurv)
  > library(pec)
  Error in library(pec) : there is no package called 'pec'
  Execution halted
Packages required but not available: ‘caret’ ‘dplyr’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘qpcR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggrepel’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘RcmdrMisc’ ‘purrr’ ‘tibble’ ‘tidyselect’
  ‘kableExtra’ ‘mice’

Package suggested but not available for checking: ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘purrr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘purrr’
Error in re-building vignettes:
  ...
Quitting from lines 330-331 (dosresmeta.Rnw) 
Error: processing vignette ‘dosresmeta.Rnw’ failed with diagnostics:
there is no package called 'rms'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘broom’ ‘dplyr’ ‘ggstance’ ‘purrr’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgbif’
Packages required but not available: ‘qpcR’ ‘readxl’

Packages suggested but not available for checking: ‘DT’ ‘ggplot2’

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

Package suggested but not available for checking: ‘nycflights13’

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

Packages suggested but not available for checking:
  ‘dbplyr’ ‘dtplyr’ ‘ggplot2’ ‘Lahman’ ‘nycflights13’

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

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 required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘drc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyselect’

Package suggested but not available for checking: ‘tidyr’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘janitor’ ‘readr’ ‘readxl’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘BIGL’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid NAMESPACE file, parsing gives:
Error in utils::packageVersion("dplyr"): package ‘dplyr’ not found

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘crosstalk’

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

Package suggested but not available for checking: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘ggrepel’

Packages suggested but not available for checking: ‘TSclust’ ‘TSdist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘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: ‘tibble’ ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking: ‘frailtyEM’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rms’ ‘plotly’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘DataCombine’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘vdiffr’ ‘incidence’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(earlyR)
  > 
  > test_check("earlyR")
  Error in library(incidence) : there is no package called 'incidence'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘tibble’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 25-28 (ebayesthresh.Rmd) 
Error: processing vignette ‘ebayesthresh.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 29-31 (ecb_sdw.Rmd) 
Error: processing vignette ‘ecb_sdw.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 49-98 (echo-vignette.Rmd) 
Error: processing vignette ‘echo-vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggmap’ ‘ggrepel’ ‘kableExtra’

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:
  ‘factoextra’ ‘viridis’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘d3heatmap’ ‘ggplot2’ ‘plotly’

Packages suggested but not available for checking: ‘adegenet’ ‘hierfstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vdiffr’
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘dplyr’ ‘Hmisc’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘dae’ ‘emmeans’ ‘ggplot2’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘bupaR’ ‘dplyr’ ‘ggplot2’ ‘ggthemes’ ‘tibble’ ‘tidyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘purrr’ ‘dplyr’ ‘tidyr’
Error in re-building vignettes:
  ...
Quitting from lines 12-18 (edgarWebR.Rmd) 
Error: processing vignette ‘edgarWebR.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘DT’ ‘tibble’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘tidyr’ ‘plotly’ ‘ggthemes’ ‘rmapshaper’

Packages suggested but not available for checking:
  ‘purrr’ ‘purrrlyr’ ‘GGally’ ‘broom’ ‘readr’

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

Packages suggested but not available for checking:
  ‘cdom’ ‘ggplot2’ ‘tidyr’ ‘DT’

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

Packages suggested but not available for checking: ‘ggplot2’ ‘tidyr’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘heplots’ ‘car’
Packages required but not available: ‘readr’ ‘dplyr’

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

Package suggested but not available for checking: ‘eggCountsExtra’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ei-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tomogRxC3d
> ### Title: Plotting 2x3 Ecological Inference Estimates in 3 dimensions
> ### Aliases: tomogRxC3d
> 
> ### ** Examples
> 
> data(RxCdata)
> formula <- cbind(turnout, noturnout) ~ cbind(white, black, hisp)
> tomogRxC3d(formula, RxCdata, total=NULL, lci=TRUE, estimates=TRUE, ci=TRUE, transparency=.5, 
+ 	light=FALSE, rotate=FALSE)
Error: Package rgl is needed for the tomogRxC3d function to work. Please install it.
Execution halted
Package required but not available: ‘qgraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘readODS’ ‘readxl’ ‘EnvStats’ ‘colourpicker’

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

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

Packages suggested but not available for checking: ‘lumi’ ‘vsn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘DataCombine’ ‘ggplot2’ ‘lmerTest’ ‘sjstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘HLMdiag’ ‘readODS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’

Packages suggested but not available for checking: ‘caret’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘bayesplot’ ‘brms’ ‘car’ ‘mediation’ ‘lmerTest’

Packages which this enhances but not available for checking:
  ‘glmmADMB’ ‘rstanarm’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘robustHD’

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

Package suggested but not available for checking: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 50-69 (GLMs.Rmd) 
Error: processing vignette ‘GLMs.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dendextend’ ‘ggplot2’ ‘ggdendro’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘drc’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘xcms’ ‘MSnbase’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘epade-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: box.plot.wtd
> ### Title: weighted Boxplot
> ### Aliases: box.plot.wtd
> ### Keywords: boxplot
> 
> ### ** Examples
> 
> x<-rnorm(1000)
> g<-round(runif(1000))
> w<-abs(rnorm(1000))
> d<- data.frame(x, g, w)
> box.plot.wtd('x', 'g', w='w', data=d)
Error in library(Hmisc) : there is no package called ‘Hmisc’
Calls: box.plot.wtd -> library
Execution halted
Package required but not available: ‘timeROC’

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

Package suggested but not available for checking: ‘readr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘ggplot2’

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

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘incidence’
Error in re-building vignettes:
  ...
Quitting from lines 122-133 (epitrix.Rmd) 
Error: processing vignette ‘epitrix.Rmd’ failed with diagnostics:
there is no package called 'incidence'
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’

Package suggested but not available for checking: ‘readr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.count’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.count’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ergm.count.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘ergm::colMeans.mcmc.list’ by ‘statnet.common::colMeans.mcmc.list’ when loading ‘ergm.ego’
  Warning: replacing previous import ‘ergm::sweep.mcmc.list’ by ‘statnet.common::sweep.mcmc.list’ when loading ‘ergm.ego’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ergm.ego.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.graphlets’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.graphlets’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ergm.graphlets.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.rank’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.rank’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ergm.rank.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.userterms’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.userterms’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ergm.userterms.Rcheck/00install.out’ for details.
Packages required but not available:
  ‘ggplot2’ ‘car’ ‘broom’ ‘dplyr’ ‘modelr’ ‘tidyr’ ‘purrr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘sjmisc’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘readr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘brms’ ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘AER’ ‘ivpack’ ‘car’

Package which this enhances but not available for checking: ‘broom’
Packages required but not available: ‘dplyr’ ‘readr’ ‘tibble’

Packages suggested but not available for checking:
  ‘dbplyr’ ‘macleish’ ‘ggplot2’

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

Packages suggested but not available for checking: ‘ggplot2’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘tidyr’ ‘readr’
Packages required but not available:
  ‘dplyr’ ‘broom’ ‘tibble’ ‘tidyr’ ‘readr’

Packages suggested but not available for checking: ‘ggplot2’ ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘readr’ ‘readxl’ ‘tibble’ ‘tidyr’ ‘viridis’

Packages suggested but not available for checking:
  ‘DT’ ‘ggalt’ ‘forcats’ ‘statip’ ‘purrrlyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tidyquant’ ‘purrr’ ‘readr’

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: ‘ggplot2’ ‘geomorph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rrepast’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘dplyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘Hmisc’ ‘tidyr’ ‘dplyr’ ‘ggplot2’ ‘DT’ ‘kableExtra’

Packages suggested but not available for checking:
  ‘gapminder’ ‘tidyquant’ ‘wbstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘smoof’
Packages required but not available: ‘DT’ ‘dplyr’ ‘tidyr’ ‘ggplot2’

Packages suggested but not available for checking: ‘FactoMineR’ ‘GDAtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘GEOquery’ ‘propr’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.

Use 'expss_output_viewer()' to display tables in the RStudio Viewer.
 To return to the console output, use 'expss_output_default()'.

Quitting from lines 56-64 (labels-support.Rmd) 
Error: processing vignette ‘labels-support.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘purrr’

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

Packages suggested but not available for checking:
  ‘dplyr’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘broom’ ‘ggplot2’ ‘tidyr’ ‘purrr’

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

Package suggested but not available for checking: ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘ggplot2’

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

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

Packages suggested but not available for checking: ‘ggplot2’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dendextend’ ‘FactoMineR’ ‘ggpubr’ ‘ggrepel’ ‘tidyr’

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: ‘car’

Package suggested but not available for checking: ‘missMDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘ggpubr’ ‘agricolae’ ‘forcats’

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

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

Package suggested but not available for checking: ‘OpenML’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘readr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggformula’ ‘mosaic’ ‘ggplot2’ ‘dplyr’

Packages suggested but not available for checking:
  ‘mosaicCalc’ ‘tidyr’ ‘readr’ ‘Hmisc’ ‘car’ ‘alr3’ ‘corrgram’

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

Packages suggested but not available for checking:
  ‘Hmisc’ ‘car’ ‘alr3’ ‘corrgram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Packages required but not available: ‘DESeq2’ ‘destiny’ ‘rgl’

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

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

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: ‘ggplot2’ ‘doBy’

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

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘plot3Drgl’ ‘rgl’
Packages suggested but not available for checking: ‘ggplot2’ ‘refund’
Package suggested but not available for checking: ‘fds’
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 in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 29-41 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'fds'
Execution halted
Packages required but not available: ‘Fgmutils’ ‘ggplot2’

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

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.
Packages required but not available:
  ‘cellranger’ ‘dplyr’ ‘googlesheets’ ‘readr’

Package suggested but not available for checking: ‘DT’

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

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘FField-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FField-package
> ### Title: Force field simulation for a set of points
> ### Aliases: FField FField-package
> ### Keywords: package
> 
> ### ** Examples
> 
> # Repel points
> coords <-
+   FFieldPtRep(coords = cbind(mtcars$wt * 100 / max(mtcars$wt), 
+                              mtcars$mpg * 100 / max(mtcars$mpg)),
+               rep.fact = 40)
> head(mtcars)
                   mpg cyl disp  hp drat    wt  qsec vs am gear carb
Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1
> head(coords)
         x        y
1 45.11259 58.47014
2 54.19136 61.20140
3 40.34714 69.42976
4 62.48920 65.94822
5 59.81417 56.33633
6 66.54832 53.33343
>   
> # Demo
> FFieldPtRepDemo()
Error in library(ggplot2) : there is no package called ‘ggplot2’
Calls: FFieldPtRepDemo -> library
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘dplyr’ ‘colorplaner’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fiftystater)
  > 
  > test_check("fiftystater")
  ── 1. Error: (unknown) (@test_fifty_states.R#1)  ───────────────────────────────
  there is no package called 'ggplot2'
  1: library(ggplot2) at testthat/test_fifty_states.R:1
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_fifty_states.R#1) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 54-76 (fiftystater.Rmd) 
Error: processing vignette ‘fiftystater.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘tibble’ ‘datadr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘diveRsity’
Packages required but not available:
  ‘klaR’ ‘ggplot2’ ‘GGally’ ‘Rcmdr’ ‘rgl’ ‘car’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 24-29 (Using_fishdata.Rmd) 
Error: processing vignette ‘Using_fishdata.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘ggthemes’
Packages required but not available: ‘DT’ ‘dplyr’

Packages suggested but not available for checking:
  ‘EnvStats’ ‘ExtDist’ ‘revdbayes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘tidyverse’ ‘broom’ ‘tidytext’ ‘ggthemes’ ‘ggraph’ ‘highcharter’
  ‘janitor’
Running examples in ‘fivethirtyeight-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ahca_polls
> ### Title: American Health Care Act Polls
> ### Aliases: ahca_polls
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # To convert data frame to tidy data (long) format, run:
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 19-30 (bechdel.Rmd) 
Error: processing vignette ‘bechdel.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Packages required but not available: ‘tibble’ ‘tidyr’

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

Packages suggested but not available for checking:
  ‘ggplot2’ ‘plotly’ ‘smoof’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggsn’ ‘ggmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘multipanelfigure’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘flowWorkspace’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘LogConcDEAD’
Packages required but not available: ‘ggplot2’ ‘tidyr’ ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tidyr’ ‘dplyr’ ‘metaplot’

Package suggested but not available for checking: ‘wrangle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘hrbrthemes’ ‘ggplot2’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forecast’ ‘ggplot2’

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

Packages suggested but not available for checking: ‘ggplot2’ ‘dtplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘expsmooth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘cowplot’

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

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘broom’ ‘tibble’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(formattable)
  > 
  > test_check("formattable")
  Failed with error:  'there is no package called 'DT''
  ── 1. Error: as.datatable (@test-render.R#18)  ─────────────────────────────────
  requireNamespace("DT") is not TRUE
  1: as.datatable(f) at testthat/test-render.R:18
  2: as.datatable.formattable(f)
  3: stopifnot(is.formattable(x), requireNamespace("DT"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 257 SKIPPED: 1 FAILED: 1
  1. Error: as.datatable (@test-render.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Failed with error:  'there is no package called 'DT''
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette ‘formattable-data-frame.Rmd’ failed with diagnostics:
requireNamespace("DT") is not TRUE
Execution halted
Package required but not available: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘FactoMineR’ ‘forcats’ ‘ggplot2’ ‘likert’ ‘tidyr’
Error in re-building vignettes:
  ...
Quitting from lines 23-31 (Overview.Rmd) 
Error: processing vignette ‘Overview.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘purrr’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 50-83 (fourierin_details.Rmd) 
Error: processing vignette ‘fourierin_details.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’ ‘mvoutlier’
Packages required but not available: ‘ggplot2’ ‘forecast’ ‘fma’ ‘expsmooth’

Packages suggested but not available for checking:
  ‘GGally’ ‘Mcomp’ ‘purrr’ ‘tidyverse’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘fractional-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: numerical
> ### Title: Convert a fractional object to the equivalent numeric object
> ### Aliases: numerical numerical.charFrac numerical.default
> ###   numerical.fractional
> 
> ### ** Examples
> 
> suppressPackageStartupMessages(library(dplyr))
Error in library(dplyr) : there is no package called ‘dplyr’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 18-26 (Theory.Rmd) 
Error: processing vignette ‘Theory.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘ggplot2’ ‘tibble’

Packages suggested but not available for checking: ‘dplyr’ ‘plotly’ ‘egg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: oro.nifti
oro.nifti 0.9.1
Quitting from lines 14-29 (exploring_included_data.Rmd) 
Error: processing vignette ‘exploring_included_data.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Package suggested but not available for checking: ‘refund’
Packages required but not available: ‘dplyr’ ‘FactoMineR’

Package suggested but not available for checking: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘Hmisc’

Packages suggested but not available for checking: ‘dggrids’ ‘INLA’

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

Packages suggested but not available for checking:
  ‘car’ ‘Hmisc’ ‘klaR’ ‘pROC’ ‘rrlda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘RTCGA.rnaseq’ ‘ggplot2’ ‘tibble’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FSelectorRcpp)
  > library(Matrix)
  > library(Rcpp)
  > library(RcppArmadillo)
  > library(dplyr)
  Error in library(dplyr) : there is no package called 'dplyr'
  Execution halted
Packages required but not available: ‘forecast’ ‘rainbow’

Packages suggested but not available for checking: ‘fds’ ‘meboot’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘rplos’ ‘rcrossref’ ‘microdemic’ ‘tibble’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘ggplot2’ ‘dplyr’

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

Packages suggested but not available for checking: ‘ggplot2’ ‘tidytext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘tidyverse’ ‘dplyr’ ‘sjmisc’
Error in re-building vignettes:
  ...
Quitting from lines 39-44 (Furniture.Rmd) 
Error: processing vignette ‘Furniture.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 64-76 (subgroup_fusion.Rmd) 
Error: processing vignette ‘subgroup_fusion.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘ggthemes’ ‘leaflet’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘purrr’

Packages suggested but not available for checking: ‘ggplot2’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’

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

Package suggested but not available for checking: ‘forecast’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘GAparsimony-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ga_parsimony
> ### Title: GA-PARSIMONY
> ### Aliases: ga_parsimony show,ga_parsimony-method
> ###   print,ga_parsimony-method print,ga_parsimony-method numericOrNA
> ### Keywords: optimize
> 
> ### ** Examples
> 
> 
> #################################
> ### Example 1: Classification ###
> #################################
> 
> # This a toy example that shows how to search, for the *iris* database, 
> # a parsimony classification NNET model with 'GAparsimony' 
> # and 'caret' packages. Validation errors and iterations have been
> # reduced to speedup the process
> 
> library(GAparsimony)
> # Training and testing Datasets
> library(caret)
Error in library(caret) : there is no package called ‘caret’
Execution halted
Package required but not available: ‘tibble’

Packages suggested but not available for checking: ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘haplo.stats’ ‘rms’
Packages required but not available: ‘dplyr’ ‘tibble’ ‘ggplot2’ ‘rstan’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Decathlon
> ### Title: Top performances in the Decathlon from 1985 to 2006.
> ### Aliases: Decathlon
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Decathlon, package="GDAdata")
> summary(Decathlon[, grep("P.*", names(Decathlon))])
   Polevault         P100m             Plj              Psp       
 Min.   :2.850   Min.   : 597.0   Min.   : 569.0   Min.   :418.0  
 1st Qu.:4.200   1st Qu.: 765.0   1st Qu.: 757.0   1st Qu.:622.0  
 Median :4.400   Median : 806.0   Median : 804.0   Median :672.0  
 Mean   :4.405   Mean   : 806.6   Mean   : 807.4   Mean   :674.6  
 3rd Qu.:4.650   3rd Qu.: 847.0   3rd Qu.: 857.0   3rd Qu.:726.0  
 Max.   :5.760   Max.   :1042.0   Max.   :1089.0   Max.   :941.0  
      Phj           P400m         P110h             Ppv              Pdt       
 Min.   : 396   Min.   :532   Min.   : 526.0   Min.   : 321.0   Min.   :231.0  
 1st Qu.: 696   1st Qu.:746   1st Qu.: 777.0   1st Qu.: 673.0   1st Qu.:600.0  
 Median : 749   Median :789   Median : 824.0   Median : 731.0   Median :655.0  
 Mean   : 749   Mean   :788   Mean   : 821.6   Mean   : 734.4   Mean   :657.8  
 3rd Qu.: 803   3rd Qu.:832   3rd Qu.: 868.0   3rd Qu.: 804.0   3rd Qu.:713.0  
 Max.   :1061   Max.   :998   Max.   :1044.0   Max.   :1152.0   Max.   :970.0  
      Pjt             P1500      
 Min.   : 330.0   Min.   :121.0  
 1st Qu.: 588.0   1st Qu.:607.0  
 Median : 644.0   Median :669.0  
 Mean   : 648.1   Mean   :661.7  
 3rd Qu.: 707.0   3rd Qu.:725.0  
 Max.   :1040.0   Max.   :946.0  
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘FactoMineR’

Package suggested but not available for checking: ‘WeightedCluster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘tibble’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘AER’ ‘ivpack’
Packages required but not available: ‘ggnetwork’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘NMF’ ‘pca3d’

Package suggested but not available for checking: ‘DESeq2’

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

Packages suggested but not available for checking: ‘genderdata’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘DataVisualizations’ ‘DatabionicSwarm’ ‘rgl’
  ‘ProjectionBasedClustering’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘leaflet’ ‘DT’ ‘purrr’ ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘tibble’ ‘forcats’
  ‘readr’ ‘rio’

Package suggested but not available for checking: ‘tidyverse’

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

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mvmesh’ ‘SphericalCubature’ ‘rgl’

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

Packages suggested but not available for checking: ‘gistr’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘geojson-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: feature
> ### Title: feature class
> ### Aliases: feature
> 
> ### ** Examples
> 
> # point -> feature
> x <- '{ "type": "Point", "coordinates": [100.0, 0.0] }'
> point(x) %>% feature()
<Feature> 
  type:  Point 
  coordinates:  [100,0] 
> 
> # multipoint -> feature
> x <- '{"type": "MultiPoint", "coordinates": [ [100.0, 0.0], [101.0, 1.0] ] }'
> multipoint(x) %>% feature()
<Feature> 
  type:  MultiPoint 
  coordinates:  [[100,0],[101,1]] 
> 
> # linestring -> feature
> x <- '{ "type": "LineString", "coordinates": [ [100.0, 0.0], [101.0, 1.0] ] }'
> linestring(x) %>% feature()
<Feature> 
  type:  LineString 
  coordinates:  [[100,0],[101,1]] 
> 
> # multilinestring -> feature
> x <- '{ "type": "MultiLineString",
+  "coordinates": [ [ [100.0, 0.0], [101.0, 1.0] ], [ [102.0, 2.0], [103.0, 3.0] ] ] }'
> multilinestring(x) %>% feature()
<Feature> 
  type:  MultiLineString 
  coordinates:  [[[100,0],[101,1]],[[102,2],[103,3]]] 
> 
> # add to a data.frame
> library('tibble')
Error in library("tibble") : there is no package called ‘tibble’
Execution halted
Running ‘test-all.R’ [3s/5s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > library("geojson")
  
  Attaching package: 'geojson'
  
  The following object is masked from 'package:graphics':
  
      polygon
  
  > test_check("geojson")
  ── 1. Error: tibbles work with multipolygon inputs (@test-tibbles.R#13)  ───────
  there is no package called 'tibble'
  1: tibble::data_frame at testthat/test-tibbles.R:13
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 259 SKIPPED: 0 FAILED: 1
  1. Error: tibbles work with multipolygon inputs (@test-tibbles.R#13) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: In expr_label(get_expr(quo)) :
    closing unused connection 7 (/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/geojson/examples/linestring_one.geojson)
  2: closing unused connection 3 (/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/geojson/examples/linestring_one.geojson) 
  Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'geojson'

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

    polygon

Quitting from lines 147-149 (geojson-operations.Rmd) 
Error: processing vignette ‘geojson-operations.Rmd’ failed with diagnostics:
there is no package called 'tibble'
Execution halted
Packages suggested but not available for checking:
  ‘ggmap’ ‘dplyr’ ‘ggplot2’
Error in re-building vignettes:
  ...
rgdal: version: 1.3-3, (SVN revision 759)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.3.0, released 2018/05/04
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.1.0, June 1st, 2018, [PJ_VERSION: 510]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-1 
Loading required package: raster

Attaching package: 'raster'

The following object is masked _by_ '.GlobalEnv':

    values<-

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

    geom, values, values<-

Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Quitting from lines 66-83 (plot_geotiff.Rmd) 
Error: processing vignette ‘plot_geotiff.Rmd’ failed with diagnostics:
there is no package called 'ggmap'
Execution halted
Packages required but not available: ‘inlmisc’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘readr’ ‘plotly’

Packages suggested but not available for checking: ‘ggrepel’ ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘purrr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tidyr’ ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘slackr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘agricolae’ ‘DT’ ‘dplyr’ ‘tibble’ ‘ggplot2’ ‘readxl’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘broom’ ‘ggplot2’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘tibble’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘readr’ ‘viridis’

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

Package suggested but not available for checking: ‘ggplot2’

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

Package suggested but not available for checking: ‘ggplot2’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tibble’ ‘dplyr’ ‘tidyr’ ‘purrr’ ‘ggplot2’ ‘plotly’ ‘ggthemes’
  ‘viridis’

Packages suggested but not available for checking:
  ‘vdiffr’ ‘pkgnet’ ‘tidyverse’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyr’ ‘scatterpie’ ‘ggplot2’ ‘ggrepel’ ‘googlesheets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘babynames’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘broom’ ‘crosstalk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tibble’ ‘plotly’

Package suggested but not available for checking: ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘purrr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘dplyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggraph’ ‘dplyr’ ‘purrr’ ‘tibble’ ‘forcats’ ‘ggrepel’
  ‘ggforce’ ‘tidygraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tibble’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggmcmc’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggforce’ ‘GGEBiplotGUI’ ‘gge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘colourpicker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘sjlabelled’ ‘sjmisc’ ‘sjstats’ ‘tibble’
  ‘tidyr’ ‘tidyselect’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘plotly’ ‘tibble’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘colourpicker’ ‘ggplot2’

Package suggested but not available for checking: ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘rstan’

Packages suggested but not available for checking: ‘tidyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘mosaicCore’ ‘tibble’

Packages suggested but not available for checking:
  ‘mosaic’ ‘dplyr’ ‘mosaicModel’ ‘broom’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘tibble’

Packages suggested but not available for checking: ‘forecast’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggfittext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘readr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘ggrepel’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggplotify’ ‘tibble’

Package suggested but not available for checking: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggiraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggridges’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘GGally’

Packages suggested but not available for checking: ‘rstan’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘productplots’ ‘plotly’ ‘dplyr’ ‘purrr’ ‘tidyr’

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

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyverse’ ‘ggplot2’ ‘dplyr’ ‘tibble’ ‘ggthemes’ ‘editData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘plotly’ ‘ggplot2’ ‘readr’ ‘haven’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘cowplot’ ‘ggimage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tibble’ ‘dplyr’ ‘broom’

Package suggested but not available for checking: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggrepel’ ‘ggsci’ ‘tidyr’ ‘purrr’ ‘dplyr’ ‘cowplot’
  ‘ggsignif’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘colourpicker’ ‘dplyr’ ‘DT’ ‘ggplot2’ ‘ggrepel’ ‘Hmisc’ ‘plotly’
  ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’

Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tidyr’

Packages suggested but not available for checking: ‘rmdformats’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘ggforce’ ‘ggrepel’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggthemes’ ‘colourpicker’ ‘dplyr’ ‘DT’ ‘GGally’ ‘tibble’

Package suggested but not available for checking: ‘RSelenium’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘dplyr’ ‘forcats’ ‘vdiffr’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘ggmap’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘photobiology’ ‘photobiologyWavebands’ ‘ggplot2’ ‘ggrepel’ ‘dplyr’
  ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘purrr’

Package suggested but not available for checking: ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘cowplot’ ‘dplyr’ ‘ggcorrplot’ ‘ggExtra’ ‘ggplot2’ ‘ggrepel’
  ‘jmv’ ‘purrr’ ‘sjstats’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘gapminder’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

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:
  ‘rstan’ ‘ggplot2’ ‘dplyr’ ‘broom’ ‘forcats’ ‘rstanarm’

Packages suggested but not available for checking: ‘bayesplot’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Attaching package: 'TMB'

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

    tmbroot

Loading required package: coda
##
## Markov Chain Monte Carlo Package (MCMCpack)
## Copyright (C) 2003-2018 Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
##
## Support provided by the U.S. National Science Foundation
## (Grants SES-0350646 and SES-0350613)
##
Quitting from lines 18-24 (mcmc.rmd) 
Error: processing vignette ‘mcmc.rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘fxregime’
Unavailable namespace imported from by a ':::' call: ‘fxregime’
  See the note in ?`:::` about the use of this operator.
Packages suggested but not available for checking: ‘forcats’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 117-117 (GMCM-JStatSoft.Rnw) 
Error: processing vignette ‘GMCM-JStatSoft.Rnw’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package suggested but not available for checking: ‘Deducer’
Package suggested but not available for checking: ‘mediation’
Error in re-building vignettes:
  ...
Loading required package: sandwich
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation

Error: processing vignette ‘gmm_with_R.rnw’ failed with diagnostics:
 chunk 14 
Error in library(car) : there is no package called ‘car’
Execution halted
Packages suggested but not available for checking: ‘AER’ ‘car’
Running examples in ‘gmnl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AIC.gmnl
> ### Title: Akaike's Information Criterion
> ### Aliases: AIC.gmnl BIC.gmnl
> 
> ### ** Examples
> 
> 
> ## Estimate MNL model
> 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
Package required but not available: ‘quanteda’

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

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
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
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘googleAnalyticsR’
Packages required but not available: ‘purrr’ ‘tibble’

Package suggested but not available for checking: ‘dplyr’

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

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘cellranger’ ‘dplyr’ ‘purrr’ ‘readr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘wbstats’
Packages required but not available: ‘ggplot2’ ‘ggdendro’

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

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

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

Package suggested but not available for checking: ‘rglwidget’

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

Package suggested but not available for checking: ‘hexSticker’

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

Package suggested but not available for checking: ‘dplyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘rtweet’ ‘purrr’

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

Packages suggested but not available for checking:
  ‘dplyr’ ‘dtplyr’ ‘ggplot2’ ‘ggrepel’ ‘taxstats’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  _t_array_properties.cpp:10:13: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gRbase.Rcheck/00install.out’ for details.
Packages required but not available: ‘Gmisc’ ‘Hmisc’ ‘rms’

Packages suggested but not available for checking: ‘dplyr’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘rms’ ‘ggplot2’

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

Packages suggested but not available for checking: ‘DiagrammeR’ ‘bayesplot’

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

Package suggested but not available for checking: ‘smooth’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘egg’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 24-33 (arrangeGrob.rmd) 
Error: processing vignette ‘arrangeGrob.rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘tidyr’ ‘broom’ ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 310-321 (Growthcurver-vignette.Rmd) 
Error: processing vignette ‘Growthcurver-vignette.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking: ‘dplyr’ ‘gsDesign’
Error in re-building vignettes:
  ...
Quitting from lines 261-285 (Introduction_gscounts.Rmd) 
Error: processing vignette ‘Introduction_gscounts.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘cellWise’

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

Packages suggested but not available for checking: ‘Hmisc’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 64-75 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘readr’ ‘tibble’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggthemes’ ‘plotKML’ ‘tidyr’

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

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

Packages suggested but not available for checking:
  ‘tidytext’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘eda4treeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mvoutlier’
Packages suggested but not available for checking: ‘nbpMatching’ ‘lmerTest’
Packages required but not available: ‘dplyr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘mnis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Read 6 items
Read 1494 items
Read 0 items
Read 8 items
Read 9112 items
Read 0 items
Read 864 items
Read 1433376 items
Read 0 items
Quitting from lines 141-142 (C_Running_Haplin.Rmd) 
Error: processing vignette ‘C_Running_Haplin.Rmd’ failed with diagnostics:
ggplot2 cannot be loaded!
Execution halted
Packages required but not available: ‘ggtree’ ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 34-37 (hazus_demo.Rmd) 
Error: processing vignette ‘hazus_demo.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘klaR’
Package suggested but not available for checking: ‘nycflights13’
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-2>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-3>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-4>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 86-92 (hdf5r.Rmd) 
Error: processing vignette ‘hdf5r.Rmd’ failed with diagnostics:
there is no package called 'nycflights13'
Execution halted
Packages required but not available: ‘rms’ ‘ggplot2’

Packages suggested but not available for checking: ‘Hmisc’ ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘caret’ ‘cowplot’ ‘dbplyr’ ‘dplyr’ ‘ggplot2’ ‘purrr’
  ‘recipes’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘plotly’ ‘viridis’ ‘ggplot2’ ‘dendextend’ ‘seriation’

Package suggested but not available for checking: ‘tidyselect’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tibble’ ‘dplyr’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tibble’

Packages suggested but not available for checking: ‘Hmisc’ ‘readxl’ ‘rgho’

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

Packages suggested but not available for checking: ‘dplyr’ ‘ggplot2’

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

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

Packages suggested but not available for checking:
  ‘rgl’ ‘candisc’ ‘corrgram’ ‘FRB’ ‘mvinfluence’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘synbreed’
Packages required but not available: ‘cplm’ ‘DESeq2’

Package suggested but not available for checking: ‘glmmADMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘hesim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: icea
> ### Title: Individualized cost-effectiveness analysis
> ### Aliases: icea icea_pw
> 
> ### ** Examples
> 
> # simulation output
> nsims <- 100
> sim <- data.frame(sim = rep(seq(nsims), 4),
+                c = c(rlnorm(nsims, 5, .1), rlnorm(nsims, 5, .1),
+                       rlnorm(nsims, 11, .1), rlnorm(nsims, 11, .1)),
+                e = c(rnorm(nsims, 8, .2), rnorm(nsims, 8.5, .1),
+                      rnorm(nsims, 11, .6), rnorm(nsims, 11.5, .6)),
+                strategy = rep(paste0("Strategy ", seq(1, 2)),
+                              each = nsims * 2),
+                grp = rep(rep(c("Group 1", "Group 2"),
+                              each = nsims), 2)
+ )
> 
> # icea
> icea.dt <- icea(sim, k = seq(0, 200000, 500), sim = "sim", strategy = "strategy",
+  grp = "grp", e = "e", c = "c")
> names(icea.dt)
[1] "summary" "mce"     "evpi"    "nmb"    
> # the probability that each strategy is the most cost-effective 
> # in each group with a willingness to pay of 20,000
> library("data.table")
> icea.dt$mce[k == 20000]
       k   strategy     grp prob
1: 20000 Strategy 1 Group 1 0.57
2: 20000 Strategy 2 Group 1 0.43
3: 20000 Strategy 1 Group 2 0.47
4: 20000 Strategy 2 Group 2 0.53
> 
> # icea_pw
> icea.pw.dt <-  icea_pw(sim,  k = seq(0, 200000, 500), comparator = "Strategy 1",
+                       sim = "sim", strategy = "strategy", e = "e", c = "c")
> names(icea.pw.dt)
[1] "summary" "delta"   "ceac"    "inmb"   
> # cost-effectiveness acceptability curve
> library("ggplot2")
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 162-170 (cea-vignette.Rmd) 
Error: processing vignette ‘cea-vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggimage’ ‘ggplot2’

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

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: ‘ggdendro’ ‘ggplot2’

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

Package suggested but not available for checking: ‘pegas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘purrr’ ‘dplyr’ ‘tibble’ ‘broom’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘highlightHTML-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: table_id_inject
> ### Title: Table hash addition for markup
> ### Aliases: table_id_inject
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(highlightHTML)
  > 
  > test_check("highlightHTML")
  ── 1. Error: add in tags to table (@test_table_id.r#4)  ────────────────────────
  there is no package called 'dplyr'
  1: library(dplyr) at testthat/test_table_id.r:4
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Error: add in tags to table (@test_table_id.r#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 118-131 (the_basics.Rmd) 
Error: processing vignette ‘the_basics.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Package required but not available: ‘rms’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘car’ ‘heplots’
Running examples in ‘HistData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Bowley
> ### Title: Bowley's data on values of British and Irish trade, 1855-1899
> ### Aliases: Bowley
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Bowley)
> 
> # plot the data 
> with(Bowley,plot(Year, Value, type='b', 
+ 	ylab="Value of British and Irish Exports",
+ 	main="Bowley's example of the method of smoothing curves"))
> 
> # find moving averages-- use center alignment (requires width=ODD)
> require(gtools, warn.conflicts=FALSE)
Loading required package: gtools
> mav3<-running(Bowley$Value, width=3, align="center")
> mav5<-running(Bowley$Value, width=5, align="center")
> mav9<-running(Bowley$Value, width=9, align="center")
> lines(Bowley$Year[2:44], mav3, col='blue', lty=2)
> lines(Bowley$Year[3:43], mav5, col='green3', lty=3)
> lines(Bowley$Year[5:41], mav9, col='brown', lty=4)
> 
> # add lowess smooth
> lines(lowess(Bowley), col='red', lwd=2)
> 
> require(ggplot2, warn.conflicts=FALSE)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> qplot(Year,Value, data=Bowley)+geom_smooth()
Error in qplot(Year, Value, data = Bowley) : 
  could not find function "qplot"
Execution halted
Packages required but not available: ‘FactoMineR’ ‘ggplot2’ ‘ggridges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘trackr’
Packages required but not available: ‘rgl’ ‘tkrgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

Packages suggested but not available for checking:
  ‘rms’ ‘mice’ ‘tables’ ‘plotly’

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

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

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

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

Packages suggested but not available for checking: ‘miceadds’ ‘Zelig’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘dplyr’ ‘vdiffr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘alr3’ ‘mice’
Package required but not available: ‘caret’

Packages suggested but not available for checking: ‘rgl’ ‘hyperSpec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘Hmisc’ ‘tibble’ ‘tidyr’ ‘dplyr’
Running ‘testInteractive.R’ [1s/1s]
  Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library('testthat')
  > 
  > test_check('htmlTable')
  Loading required package: htmlTable
  ── 1. Error: HTML code is properly escaped (@test-htmlTable.R#398)  ────────────
  there is no package called 'tibble'
  1: tibble::as.tibble at testthat/test-htmlTable.R:398
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 455 SKIPPED: 1 FAILED: 1
  1. Error: HTML code is properly escaped (@test-htmlTable.R#398) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 101-141 (tables.Rmd) 
Error: processing vignette ‘tables.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package suggested but not available for checking: ‘tidyr’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
No encoding supplied: defaulting to UTF-8.
Quitting from lines 47-50 (htmltab.Rmd) 
Error: processing vignette ‘htmltab.Rmd’ failed with diagnostics:
there is no package called 'tidyr'
Execution halted
Package suggested but not available for checking: ‘HTSFilter’
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘DESeq2’ ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘GGally’ ‘EnvStats’ ‘viridis’
Package suggested but not available for checking: ‘tidyverse’
Error in re-building vignettes:
  ...
Quitting from lines 28-39 (ivs-sh.Rmd) 
Error: processing vignette ‘ivs-sh.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggmap’ ‘ggplot2’ ‘purrr’ ‘tidyr’

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:
  ‘dplyr’ ‘nycflights13’ ‘ggplot2’
Packages required but not available: ‘dplyr’ ‘tibble’ ‘tidyselect’

Packages suggested but not available for checking: ‘broom’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘adegenet’
Running examples in ‘HWxtest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hwx.test
> ### Title: Test for HW by either full enumeration or Monte Carlo.
> ### Aliases: hwx.test
> 
> ### ** Examples
> 
> # Data from Louis and Dempster 1987 Table 2 and Guo and Thompson 1992 Figure 2:
> c <- c(0,3,1,5,18,1,3,7,5,2)
> hwx.test(c)

*****    Sample of 45 diploids with 4 alleles
Full enumeration of 162365 tables to test for HW

P value (LLR)   = 0.012945
P value (Prob)  = 0.017442
P value (U)     = 0.003343 (test for heterozygote excess)
P value (Chisq) = 0.020170
> # To see a histogram of the LLR statistic:
> hwx.test(c, histobins=TRUE)

*****    Sample of 45 diploids with 4 alleles
Full enumeration of 162365 tables to test for HW

P value (LLR)   = 0.012945
P value (Prob)  = 0.017442
P value (U)     = 0.003343 (test for heterozygote excess)
P value (Chisq) = 0.020170
Loading required namespace: ggplot2
Failed with error:  ‘there is no package called ‘ggplot2’’
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 6-18 (HWxtest.Rmd) 
Error: processing vignette ‘HWxtest.Rmd’ failed with diagnostics:
there is no package called 'adegenet'
Execution halted
Package required but not available: ‘InformationValue’

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

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

Packages suggested but not available for checking:
  ‘dataRetrieval’ ‘ggplot2’ ‘kableExtra’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘hydrostats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flood.length.max
> ### Title: Calculates the maximum flood length in a time series.
> ### Aliases: flood.length.max
> 
> ### ** Examples
> 
> 
> data(Cooper)
> Cooper<-ts.format(Cooper)
> 
> flood.length.max(Cooper, threshold = 50000, ind.days = 5)
  max.duration
1           40
> 
> # Return annual maximum flood length based on calendar year using ddply (from plyr package) 
> require(plyr)
Loading required package: plyr
> Cooper$Year=format(Cooper$Date, format="%Y")
> ddply(Cooper, .(Year), flood.length.max, threshold = 50000)
   Year max.duration
1  1967            0
2  1968           13
3  1969            0
4  1970            0
5  1971           10
6  1972            6
7  1973           17
8  1974           40
9  1975            2
10 1976           21
11 1977           19
12 1978            0
13 1979            8
14 1980            1
15 1981            3
16 1982            0
17 1983           10
18 1984            0
19 1985            0
20 1986            7
21 1987            0
> 
> require(dplyr)
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘dplyr’
> Cooper %>%
+ dplyr::group_by(Year) %>%
+ dplyr::do(flood.length.max(., threshold = 50000))
Error in Cooper %>% dplyr::group_by(Year) %>% dplyr::do(flood.length.max(.,  : 
  could not find function "%>%"
Execution halted
Package required but not available: ‘unbalanced’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IalsaSynthesis)
  > 
  > test_check("IalsaSynthesis")
  ── 1. Error: (unknown) (@test-extract.R#8)  ────────────────────────────────────
  there is no package called 'readr'
  1: readr::read_file at testthat/test-extract.R:8
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-extract.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘dplyr’ ‘qgraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘SparkR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dynsurv’
Packages required but not available:
  ‘car’ ‘coefplot’ ‘forecast’ ‘openair’ ‘papeR’

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

Packages suggested but not available for checking: ‘tidyr’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘rstan’ ‘dplyr’ ‘tidyr’ ‘bayesplot’ ‘ggplot2’ ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DendSer’
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘FRK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggrepel’

Package suggested but not available for checking: ‘caret’

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

Packages suggested but not available for checking: ‘ie2miscdata’ ‘iemisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘iemisc’ ‘ie2misc’ ‘ie2miscdata’ ‘qdap’
Packages required but not available: ‘listless’ ‘IAPWS95’

Packages suggested but not available for checking:
  ‘ie2misc’ ‘financial’ ‘optiRum’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘NSM3’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dae’ ‘ggplot2’ ‘Hmisc’ ‘GGally’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘caret’ ‘lime’ ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘dbplyr’ ‘tidyselect’

Packages suggested but not available for checking: ‘Lahman’ ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘importar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: import
> ### Title: This function imports/loads packages as in 'Python', i.e.,
> ###   "import package as alias"
> ### Aliases: import
> 
> ### ** Examples
> 
> import(dplyr, d)
Error in library(package., character.only = TRUE) : 
  there is no package called ‘dplyr’
Calls: import -> <Anonymous> -> withCallingHandlers -> library
Execution halted
Packages required but not available: ‘Hmisc’ ‘haven’

Package suggested but not available for checking: ‘compareGroups’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘forecast’ ‘ggplot2’ ‘imputeTS’ ‘tidyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘cowplot’ ‘dplyr’ ‘drc’ ‘DT’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘cowplot’ ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tibble’ ‘tidyr’ ‘vdiffr’

Package suggested but not available for checking: ‘ggdendro’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘iNEXT’

Package suggested but not available for checking: ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘ggplot2’

Packages suggested but not available for checking: ‘broom’ ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘descriptr’ ‘haven’ ‘readr’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘minfi’
Package suggested but not available for checking: ‘dbplyr’
Error in re-building vignettes:
  ...
Quitting from lines 157-158 (getting_started.Rmd) 
Error: processing vignette ‘getting_started.Rmd’ failed with diagnostics:
there is no package called 'dbplyr'
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘ggmap’ ‘rgl’ ‘sphereplot’ ‘dplyr’ ‘INLA’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘FactoMineR’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 16-23 (interlineaR.Rmd) 
Error: processing vignette ‘interlineaR.Rmd’ failed with diagnostics:
there is no package called 'kableExtra'
Execution halted
Packages required but not available: ‘ggplot2’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > library(io)
  Loading required package: filenamer
  > 
  > test_check("io")
  ── 1. Error: (unknown) (@test_read-write-read.R#8)  ────────────────────────────
  no applicable method for 'h5write' applied to an object of class "character"
  1: test_read_write_read(f) at testthat/test_read-write-read.R:8
  2: qwrite(x, outfile) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/io.Rcheck/tests/testthat/helper.R:48
  3: .qwrite(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  4: qwrite.hdf5(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  5: .write_hdf5_array(x, file)
  6: rhdf5::h5write("array", file, "type")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘dplyr’ ‘eurostat’ ‘tidyr’ ‘forcats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘haven’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking: ‘DT’ ‘ggplot2’

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

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Fgmutils’ ‘rbokeh’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘cowplot’ ‘ggplot2’ ‘GGally’ ‘xergm’ ‘comtradr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘NMF’
Error in re-building vignettes:
  ...
Quitting from lines 45-47 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'NMF'
Execution halted
Packages required but not available: ‘qvalue’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘janeaustenr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: austen_books
> ### Title: Tidy data frame of Jane Austen's 6 completed, published novels
> ### Aliases: austen_books
> 
> ### ** Examples
> 
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(janeaustenr)
  > 
  > test_check("janeaustenr")
  ── 1. Error: (unknown) (@test_austen_books.R#5)  ───────────────────────────────
  there is no package called 'dplyr'
  1: suppressPackageStartupMessages(library(dplyr)) at testthat/test_austen_books.R:5
  2: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
  3: library(dplyr)
  4: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_austen_books.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘iClick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘jiebaR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_list
> ### Title: Apply list input to a worker
> ### Aliases: apply_list
> 
> ### ** Examples
> 
> cutter = worker()
Error in unzip(file.path(jiebapath, "dict", "jieba.dict.zip"), exdir = file.path(jiebapath,  : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/jieba.dict.utf8': Read-only file system
Error in unzip(file.path(jiebapath, "dict", "hmm_model.zip"), exdir = file.path(jiebapath,  : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/hmm_model.utf8': Read-only file system
Error in unzip(file.path(jiebapath, "dict", "idf.zip"), exdir = file.path(jiebapath,  : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/idf.utf8': Read-only file system
2018-06-25 17:48:10 ../inst/include/lib/DictTrie.hpp:159 FATAL exp: [ifs.is_open()] false. open /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/jieba.dict.utf8 failed.
terminate called after throwing an instance of 'Rcpp::exception'
  what():  2018-06-25 17:48:10 ../inst/include/lib/DictTrie.hpp:159 FATAL exp: [ifs.is_open()] false. open /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/jieba.dict.utf8 failed.
Aborted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("jiebaR")
  Loading required package: jiebaR
  Loading required package: jiebaRD
  Error in unzip(file.path(jiebapath, "dict", "jieba.dict.zip"), exdir = file.path(jiebapath,  : 
    cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/jieba.dict.utf8': Read-only file system
  Error in unzip(file.path(jiebapath, "dict", "hmm_model.zip"), exdir = file.path(jiebapath,  : 
    cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/hmm_model.utf8': Read-only file system
  Error in unzip(file.path(jiebapath, "dict", "idf.zip"), exdir = file.path(jiebapath,  : 
    cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/idf.utf8': Read-only file system
  2018-06-25 17:48:12 ../inst/include/lib/DictTrie.hpp:159 FATAL exp: [ifs.is_open()] false. open /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/jieba.dict.utf8 failed.
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  2018-06-25 17:48:12 ../inst/include/lib/DictTrie.hpp:159 FATAL exp: [ifs.is_open()] false. open /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/jieba.dict.utf8 failed.
  Aborted
Error in re-building vignettes:
  ...
Error in unzip(file.path(jiebapath, "dict", "jieba.dict.zip"), exdir = file.path(jiebapath,  : 
  cannot open file ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/jieba.dict.utf8’: Read-only file system
Error in unzip(file.path(jiebapath, "dict", "hmm_model.zip"), exdir = file.path(jiebapath,  : 
  cannot open file ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/hmm_model.utf8’: Read-only file system
Error in unzip(file.path(jiebapath, "dict", "idf.zip"), exdir = file.path(jiebapath,  : 
  cannot open file ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/idf.utf8’: Read-only file system
2018-06-25 17:48:14 ../inst/include/lib/DictTrie.hpp:159 FATAL exp: [ifs.is_open()] false. open /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/jieba.dict.utf8 failed.
terminate called after throwing an instance of 'Rcpp::exception'
  what():  2018-06-25 17:48:14 ../inst/include/lib/DictTrie.hpp:159 FATAL exp: [ifs.is_open()] false. open /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/jiebaRD/dict/jieba.dict.utf8 failed.
Aborted
Packages required but not available: ‘rstan’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘car’ ‘ggplot2’ ‘emmeans’ ‘GGally’ ‘afex’ ‘ggridges’

Package suggested but not available for checking: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘JointAI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: md_pattern
> ### Title: Missing data pattern
> ### Aliases: md_pattern
> 
> ### ** Examples
> 
> md_pattern(wideDF)
Error in md_pattern(wideDF) : 
  This function requires the 'mice' package to be installed.
Execution halted
Packages suggested but not available for checking: ‘BaBooN’ ‘mitml’
Packages required but not available:
  ‘dplyr’ ‘leaflet’ ‘purrr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘jpmesh’ ‘dplyr’ ‘leaflet’ ‘purrr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘broom’ ‘brms’ ‘cowplot’ ‘ggstance’ ‘huxtable’ ‘rstanarm’ ‘weights’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘cowplot’ ‘Hmisc’ ‘mice’

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

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘clustMD’ ‘ggplot2’ ‘Hmisc’
Packages required but not available:
  ‘MVN’ ‘forecast’ ‘nonlinearTseries’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘tidytext’
Error in re-building vignettes:
  ...
Quitting from lines 13-26 (methods.Rmd) 
Error: processing vignette ‘methods.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘EnvStats’ ‘tibble’

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

Packages suggested but not available for checking: ‘tensorflow’ ‘ggplot2’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: knitr
Loading required package: kfigr
knitr hook "anchor" is now available
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Quitting from lines 26-28 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
could not find function "qplot"
Execution halted
Package required but not available: ‘questionr’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 17-32 (cars.Rmd) 
Error: processing vignette ‘cars.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(knitrProgressBar)
  > library(mockr)
  
  Attaching package: 'mockr'
  
  The following object is masked from 'package:testthat':
  
      with_mock
  
  > library(withr)
  > 
  > test_check("knitrProgressBar")
  Read 7 items
  Read 7 items
  ── 1. Error: regular progress works (@test-kpb.R#14)  ──────────────────────────
  there is no package called 'purrr'
  1: with_mock(is_interactive = function() TRUE, is_in_knitr = function() FALSE, {
         pb <- progress_estimated(5)
         withr::with_output_sink("test_pb.txt", run_pb())
         expect_match(scan("test_pb.txt", what = character(), quiet = TRUE), "|========================================================================================================|100% ~0 s remaining")
         file.remove("test_pb.txt")
     }) at testthat/test-kpb.R:14
  2: with_mock_(.dots = .dots, .parent = .parent, .env = .env)
  3: evaluate_with_mock_env(get_code_dots(dots), mock_env, .parent)
  4: lazyeval::lazy_eval(code[[length(code)]])
  5: eval(x$expr, x$env, emptyenv())
  6: eval(x$expr, x$env, emptyenv())
  7: withr::with_output_sink("test_pb.txt", run_pb()) at testthat/test-kpb.R:20
  8: force(code)
  9: run_pb()
  10: purrr::map at testthat/test-kpb.R:6
  11: getExportedValue(pkg, name)
  12: asNamespace(ns)
  13: getNamespace(ns)
  14: tryCatch(loadNamespace(name), error = function(e) stop(e))
  15: tryCatchList(expr, classes, parentenv, handlers)
  16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  17: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 16 SKIPPED: 0 FAILED: 1
  1. Error: regular progress works (@test-kpb.R#14) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  closing unused connection 4 (kpb_output.log) 
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 131-134 (example_progress_bars.Rmd) 
Error: processing vignette ‘example_progress_bars.Rmd’ failed with diagnostics:
there is no package called 'purrr'
Execution halted
Packages suggested but not available for checking: ‘rgl’ ‘tibble’
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘KODAMA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dinisurface
> ### Title: Ulisse Dini Data Set Generator
> ### Aliases: dinisurface
> ### Keywords: dataset
> 
> ### ** Examples
> 
> require("rgl")
Loading required package: rgl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgl’
> x=dinisurface()
> open3d()
Error in open3d() : could not find function "open3d"
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tidyr’

Package suggested but not available for checking: ‘forcats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Error in re-building vignettes:
  ...
Quitting from lines 24-28 (copper_mining_2d.Rmd) 
Error: processing vignette ‘copper_mining_2d.Rmd’ failed with diagnostics:
there is no package called 'plotly'
Execution halted
Package suggested but not available for checking: ‘FactoClass’
Packages suggested but not available for checking: ‘OceanView’ ‘rgl’
Running examples in ‘ks-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.kdde
> ### Title: Plot for kernel density derivative estimate
> ### Aliases: plot.kdde
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ## univariate example
> data(tempb)
> fhat1 <- kdde(x=tempb[,"tmin"], deriv.order=1)   ## gradient [df/dx, df/dy]
> plot(fhat1, xlab="Min. temp.")                   ## df/dx
> points(20,predict(fhat1, x=20))
> 
> ## bivariate example
> fhat1 <- kdde(x=tempb[,c("tmin", "tmax")], deriv.order=1)
> plot(fhat1, display="quiver")
Error: Install the OceanView package as it is required.
Execution halted
Package suggested but not available for checking: ‘rockchalk’
Packages required but not available: ‘haven’ ‘dplyr’

Package suggested but not available for checking: ‘questionr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 124-133 (labelVector.Rmd) 
Error: processing vignette ‘labelVector.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package suggested but not available for checking: ‘crs’
Packages required but not available: ‘GGally’ ‘ggplot2’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tibble’ ‘tidyr’ ‘viridis’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rgl’ ‘heplots’
Found the following significant warnings:
  Warning: replacing previous import ‘ergm::colMeans.mcmc.list’ by ‘statnet.common::colMeans.mcmc.list’ when loading ‘latentnet’
  Warning: replacing previous import ‘ergm::sweep.mcmc.list’ by ‘statnet.common::sweep.mcmc.list’ when loading ‘latentnet’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/latentnet.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 55-71 (using-latex2exp.Rmd) 
Error: processing vignette ‘using-latex2exp.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘lmerTest’ ‘riskRegression’

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

Package which this enhances but not available for checking: ‘geojsonio’
Running examples in ‘lawn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lawn_unkinkpolygon
> ### Title: Unkink polygon
> ### Aliases: lawn_unkinkpolygon
> 
> ### ** Examples
> 
> x <- '{
+   "type": "Feature",
+   "properties": {},
+   "geometry": {
+     "type": "Polygon",
+       "coordinates": [[[0, 0], [2, 0], [0, 2], [2, 2], [0, 0]]]
+    }
+ }'
> lawn_unkinkpolygon(x)
<FeatureCollection>
  Bounding box: 0.0 0.0 2.0 2.0
  No. features: 2
  No. points: 16
  Properties: NULL
> view(x)
Error: Please install leaflet
Execution halted
Package required but not available: ‘weights’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gistr’
Error in re-building vignettes:
  ...
Loading required package: grid
Loading required package: survival
Loading required package: Matrix
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘addTracks.Rnw’ failed with diagnostics:
 chunk 14 (label = addQplot) 
Error in ggplotGrob({ : could not find function "ggplotGrob"
Execution halted
Packages required but not available: ‘ecd’ ‘ggplot2’

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

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

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

Package suggested but not available for checking: ‘readr’

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

Package suggested but not available for checking: ‘dplyr’

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

Package suggested but not available for checking: ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Error: processing vignette ‘LEAP_Vignette.Rnw’ failed with diagnostics:
 chunk 10 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘ggplot2’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘Rcmdr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘dplyr’ ‘tidyverse’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mapview’ ‘mapedit’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘demography’ ‘forecast’
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lifecontingencies.Rcheck/vign_test/lifecontingencies") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/pensionfunding.Rmd’
(Is a VignetteBuilder field missing?)
Package:  lifecontingencies
Authors:  Giorgio Alfredo Spedicato [cre,aut], Reinhold Kainhofer [ctb], Kevin J.
    Owens [ctb], Christophe Dutang [ctb], Ernesto Schirmacher[ctb], Gian Paolo Clemente [ctb]
Version:  1.3.2
Date:     2017-12-09
BugReport: http://github.com/spedygiorgio/lifecontingencies/issues

Loading required package: markovchain
Package:  markovchain
Version:  0.6.9.10
Date:     2018-06-01
BugReport: http://github.com/spedygiorgio/markovchain/issues

Loading required package: parallel

Error: processing vignette ‘mortality_projection.Rnw’ failed with diagnostics:
 chunk 2 (label = load) 
Error in library(demography) : there is no package called 'demography'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘modelr’ ‘tidyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘mlr’ ‘keras’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘mlr’
Packages suggested but not available for checking: ‘tibble’ ‘purrr’
Packages required but not available:
  ‘mlr’ ‘dplyr’ ‘breakDown’ ‘forestmodel’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mlr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘lle-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_lle
> ### Title: Plot LLE results
> ### Aliases: plot_lle
> 
> ### ** Examples
> 
> 	data( lle_scurve_data )
> 	X <- lle_scurve_data
> 	Y <- lle( X, m=2, k=12 )$Y
finding neighbours
calculating weights
computing coordinates
> 	plot_lle( Y, X, FALSE, col="red", inter=TRUE )
Loading required package: rgl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgl’
Error in plot3d(Y, col = col) : could not find function "plot3d"
Calls: plot_lle
Execution halted
Package required but not available: ‘ggtern’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: Matrix
Quitting from lines 95-111 (lmer.Rnw) 
Error: processing vignette ‘lmer.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘SPEI’
Packages suggested but not available for checking: ‘car’ ‘dynlm’ ‘AER’
Packages suggested but not available for checking: ‘dendextend’ ‘ggplot2’
Error in re-building vignettes:
  ...

Error: processing vignette ‘LocalControl-jss-2018.Rnw’ failed with diagnostics:
 chunk 2 (label = init_libs_vars_calcs) 
Error in library(dendextend) : there is no package called 'dendextend'
Execution halted
Package suggested but not available for checking: ‘mosaic’
Packages required but not available: ‘rms’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 7-30 (logitnorm.Rmd) 
Error: processing vignette ‘logitnorm.Rmd’ failed with diagnostics:
could not find function "exit"
Execution halted
Packages suggested but not available for checking: ‘rgl’ ‘RDRToolbox’
Packages suggested but not available for checking:
  ‘bayesplot’ ‘rstan’ ‘rstanarm’
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(loo)
  This is loo version 2.0.0.
  **NOTE: As of version 2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. Visit mc-stan.org/loo/news for details on other changes.
  
  Attaching package: 'loo'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > Sys.setenv("R_TESTS" = "")
  > test_check("loo")
  ── 1. Error: (unknown) (@test_psis.R#2)  ───────────────────────────────────────
  there is no package called 'rstanarm'
  1: suppressPackageStartupMessages(library(rstanarm)) at testthat/test_psis.R:2
  2: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
  3: library(rstanarm)
  4: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 341 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_psis.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘shapes’ ‘rgl’

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

Package suggested but not available for checking: ‘tidyr’

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

Packages suggested but not available for checking:
  ‘BIFIEsurvey’ ‘miceadds’ ‘mice’ ‘car’ ‘mitml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘car’ ‘mediation’ ‘glmmADMB’ ‘lmerTest’ ‘rstan’ ‘rstanarm’
Packages suggested but not available for checking: ‘ggplot2’ ‘broom’
Error in re-building vignettes:
  ...
Quitting from lines 69-75 (lspline.Rmd) 
Error: processing vignette ‘lspline.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggmcmc’ ‘ggplot2’
Error in re-building vignettes:
  ...
Loading required package: mcmc
Loading required package: MHadaptive
Loading required package: MASS
Loading required package: numDeriv
Quitting from lines 13-17 (example-plots.Rmd) 
Error: processing vignette ‘example-plots.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘broom’ ‘dplyr’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: lucid
Loading required package: lattice
Quitting from lines 190-193 (lucid_printing.Rmd) 
Error: processing vignette ‘lucid_printing.Rmd’ failed with diagnostics:
could not find function "%>%"
Execution halted
Packages suggested but not available for checking: ‘caret’ ‘Hmisc’
Running examples in ‘lulcc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: allow
> ### Title: Implement decision rules for land use change
> ### Aliases: allow
> 
> ### ** Examples
> 
> 
> ## Plum Island Ecosystems
> 
> ## load observed land use data
> obs <- ObsLulcRasterStack(x=pie,
+                    pattern="lu",
+                    categories=c(1,2,3),
+                    labels=c("forest","built","other"),
+                    t=c(0,6,14))
> 
> ## get land use values
> x <- getValues(obs[[1]])
> x <- x[!is.na(x)]
> 
> ## create vector of arbitrary land use history values
> hist <- sample(1:10, length(x), replace=TRUE)
> 
> ## calculate demand and get change direction for first timestep
> dmd <- approxExtrapDemand(obs=obs, tout=0:14)
Warning in total(x = obs) :
  missing argument 'categories': getting categories from 'x'
Error in loadNamespace(name) : there is no package called ‘Hmisc’
Calls: approxExtrapDemand ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package required but not available: ‘readxl’

Packages suggested but not available for checking:
  ‘RLumShiny’ ‘RLumModel’ ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘depth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘caret’

Packages suggested but not available for checking: ‘moveHMM’ ‘DiagrammeR’

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

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

Packages suggested but not available for checking:
  ‘ggplot2’ ‘dbplyr’ ‘broom’ ‘ggmap’ ‘leaflet’ ‘clifro’

VignetteBuilder packages required for checking but not installed:
  ‘etl’ ‘dplyr’ ‘ggplot2’ ‘leaflet’ ‘clifro’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘R2wd’
Error in re-building vignettes:
  ...
Quitting from lines 33-38 (maddison_project_database.Rmd) 
Error: processing vignette ‘maddison_project_database.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘R2wd’ ‘ggplot2’
Packages required but not available:
  ‘forecast’ ‘forecastHybrid’ ‘ggplot2’ ‘tidyr’ ‘ggseas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘imager’
Packages suggested but not available for checking:
  ‘ggplot2’ ‘gapminder’ ‘tesseract’
Running examples in ‘magick-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: device
> ### Title: Magick Graphics Device
> ### Aliases: device image_graph image_device image_draw image_capture
> 
> ### ** Examples
> 
> # Regular image
> frink <- image_read("https://jeroen.github.io/images/frink.png")
> 
> # Produce image using graphics device
> fig <- image_graph(res = 96)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = cyl)
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 414-418 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘GEOquery’ ‘GEOmetadb’ ‘beadarray’ ‘lumi’ ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘DT’

Packages suggested but not available for checking: ‘haven’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘leaflet’ ‘plotly’
Packages required but not available: ‘forecast’ ‘smooth’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘leaflet’ ‘spocc’ ‘gistr’

Packages suggested but not available for checking: ‘ggmap’ ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 95-100 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘gapminder’

Package which this enhances but not available for checking: ‘AER’
Error in re-building vignettes:
  ...
Quitting from lines 347-355 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘biomod2’
Error in re-building vignettes:
  ...
Loading required package: lme4
Loading required package: Matrix
Loading required package: parallel
This is marked 1.2.1


Error: processing vignette ‘markedVignette.Rnw’ failed with diagnostics:
 chunk 4 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages suggested but not available for checking:
  ‘broom’ ‘ggplot2’ ‘Hmisc’
Running examples in ‘MARSS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: augment.marssMLE
> ### Title: Return the model predicted values, residuals, and optionally
> ###   confidence intervals
> ### Aliases: augment.marssMLE augment_dfa augment_marss augmentmarxss
> 
> ### ** Examples
> 
>   dat <- t(harborSeal)
>   dat <- dat[c(2,11,12),]
>   MLEobj <- MARSS(dat, model=list(Z=factor(c("WA","OR","OR"))))
Success! abstol and log-log tests passed at 37 iterations.
Alert: conv.test.slope.tol is 0.5.
Test with smaller values (<0.1) to ensure convergence.

MARSS fit is
Estimation method: kem 
Convergence test: conv.test.slope.tol = 0.5, abstol = 0.001
Estimation converged in 37 iterations. 
Log-likelihood: 13.72233 
AIC: -11.44465   AICc: -8.918339   
 
                Estimate
A.OR.SouthCoast  0.49280
R.diag           0.02509
U.WA             0.06171
U.OR             0.03686
Q.(WA,WA)        0.01082
Q.(OR,OR)        0.00439
x0.WA            7.41712
x0.OR            6.56460
Initial states (x0) defined at t=0

Standard errors have not been calculated. 
Use MARSSparamCIs to compute CIs and bias estimates.

> 
> library(broom)
Error in library(broom) : there is no package called ‘broom’
Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 65-75 (././Sections/4_MonteCarloResults.Rnw) 
Quitting from lines 39-40 (././Sections/4_MonteCarloResults.Rnw) 
Error: processing vignette ‘matching.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘WhatIf’
Packages required but not available: ‘weights’ ‘Hmisc’

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

Package suggested but not available for checking: ‘rglwidget’

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

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘extracat’ ‘dplyr’ ‘seriation’ ‘ggplot2’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spsurvey’
Error in re-building vignettes:
  ...
Quitting from lines 187-200 (MBHdesign.Rnw) 
Error: processing vignette ‘MBHdesign.Rnw’ failed with diagnostics:
there is no package called 'spsurvey'
Execution halted
Packages required but not available: ‘rstan’ ‘overlapping’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ecr’ ‘ggplot2’

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

Depends: includes the non-default packages:
  ‘lattice’ ‘locfit’ ‘maptools’ ‘quantreg’ ‘RANN’ ‘SparseM’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running examples in ‘McSpatial-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gmmprobit 
> ### Title: GMM Spatial Probit
> ### Aliases: 'gmmprobit '
> ### Keywords: Parmametric Models Spatial AR Model Discrete Choice Models
> 
> ### ** Examples
> 
> set.seed(9947)
> cmap <- readShapePoly(system.file("maps/CookCensusTracts.shp",
+   package="McSpatial"))
Warning: use rgdal::readOGR or sf::st_read
> cmap <- cmap[cmap$CHICAGO==1&cmap$CAREA!="O'Hare",]
> lmat <- coordinates(cmap)
> dnorth <- geodistance(lmat[,1],lmat[,2], -87.627800, 
+ 	41.881998, dcoor=TRUE)$dnorth
> cmap <- cmap[dnorth>0,]
> wmat <- makew(cmap)$wmat
Loading required package: Matrix
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`
> n = nrow(wmat)
> rho = .4
> x <- runif(n,0,10)
> ystar <- as.numeric(solve(diag(n) - rho*wmat)%*%(x + rnorm(n,0,2)))
> y <- ystar>quantile(ystar,.4)
> fit <- gmmprobit(y~x,  wmat=wmat)
Error in library(car) : there is no package called ‘car’
Calls: gmmprobit -> library
Execution halted
Package required but not available: ‘miceadds’

Package suggested but not available for checking: ‘mice’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘babynames’ ‘dbplyr’ ‘dplyr’ ‘ggplot2’ ‘mosaic’

Packages suggested but not available for checking:
  ‘Lahman’ ‘etl’ ‘macleish’

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

Package suggested but not available for checking: ‘car’

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

Package suggested but not available for checking: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 50-60 (advanced.Rmd) 
Error: processing vignette ‘advanced.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 61-67 (cost-report-analysis.Rmd) 
Error: processing vignette ‘cost-report-analysis.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Package required but not available: ‘Hmisc’

Depends: includes the non-default packages:
  ‘seqinr’ ‘pcaMethods’ ‘Matrix’ ‘ROCR’ ‘Hmisc’ ‘KernSmooth’ ‘seqLogo’
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: ‘purrr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘leaflet’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyr’ ‘dplyr’ ‘haven’ ‘readxl’ ‘DT’ ‘ggplot2’ ‘plotly’ ‘mem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘cowplot’ ‘ggimage’ ‘shadowtext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘cowplot’ ‘purrr’ ‘colourpicker’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: codomToPropShared
> ### Title: Find proportion of shared alleles genetic distances from a
> ###   codominant alleles matrix
> ### Aliases: codomToPropShared
> 
> ### ** Examples
> 
> 
> radialData <- read.csv(system.file("extdata/radial.csv", package="memgene"))
> radialGen <- radialData[, -c(1,2)]
> radialDM <- codomToPropShared(radialGen)
Loading required package: adegenet
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘adegenet’
Error: memgene:  Please install the adegenet package to find the proportion of shared alleles
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 21-30 (memgeneTutorial.Rnw) 
Error: processing vignette ‘memgeneTutorial.Rnw’ failed with diagnostics:
there is no package called 'adegenet'
Execution halted
Packages which this enhances but not available for checking: ‘AER’ ‘car’
Packages required but not available: ‘ggplot2’ ‘tidyr’ ‘dplyr’ ‘EnvStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘DT’ ‘ggplot2’ ‘broom’

Package suggested but not available for checking: ‘rstanarm’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘taxa’ ‘ggplot2’ ‘taxize’ ‘traits’ ‘dplyr’ ‘readr’ ‘ggfittext’
  ‘ggrepel’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘preprocomb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GEOquery’ ‘GEOmetadb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘forcats’ ‘ggplot2’ ‘purrr’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GEOquery’
Packages suggested but not available for checking: ‘GEOquery’ ‘doSMP’
Packages suggested but not available for checking: ‘HTSFilter’ ‘DESeq2’
Error in re-building vignettes:
  ...

Error: processing vignette ‘metaRNASeq.Rnw’ failed with diagnostics:
 chunk 2 (label = loadparameters) 
Error in library(DESeq2) : there is no package called ‘DESeq2’
Execution halted
Package suggested but not available for checking: ‘semPlot’
Running examples in ‘MetaSubtract-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meta.subtract
> ### Title: Subtracts GWAS results from one or more cohorts from the
> ###   meta-GWAS results
> ### Aliases: meta.subtract
> ### Keywords: Correct meta-GWAS results Leave-one-out
> 
> ### ** Examples
> 
> metafile="meta_results.txt"
> cohortfiles=c("cohort1_results.txt","cohort2_results.txt","cohort3_results.txt")
> # Subtract summary statistics of the two cohorts from the meta summary statistics in metafile.
> # Genomic control correction of the imported meta summary statistics will be undone using 
> # lambda.meta. Genomic control will be applied to the corrected meta summary statistics 
> # (gc_meta=TRUE by default) based on a lambda derived from the new meta summary statistics 
> # (calculate_lambda.meta=TRUE by default). The cohorts summary statistics will always be first 
> # corrected for genomic control before subtracting them from the meta summary statistics. By 
> # default, the lambda will be calculated from the data (calculate_lambdas.cohort=TRUE by default).
> m1<-meta.subtract(metafile=metafile, cohortfiles=cohortfiles, lambda.meta=1.046, dir=tempdir())
Analysis started Mon Jun 25 16:17:34 2018 
Reading /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MetaSubtract/extdata/meta_results.txt 
Subtracting effects of /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MetaSubtract/extdata/cohort1_results.txt  
 - Number of genetic markers removed because of mismatch in alleles: 1 (0.12%)  
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MetaSubtract/extdata/cohort1_results.txt.allele_mismatch.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: meta.subtract -> write.table -> file
Execution halted
Packages required but not available: ‘ggplot2’ ‘nullabor’ ‘dplyr’ ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘metricsgraphics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mjs_add_confidence_band
> ### Title: Add a confidence band to line plot
> ### Aliases: mjs_add_confidence_band
> 
> ### ** Examples
> 
> require(binom)
Loading required package: binom
> require(dplyr)
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘dplyr’
> 
> set.seed(1492)
> binom.confint(x=sample(2:30, 100, replace=TRUE), n = 100, tol = 1e-8,
+               methods="bayes") %>%
+   mutate(x=1:100) -> bdat
Error in mutate(., x = 1:100) : could not find function "mutate"
Calls: %>% ... eval -> _fseq -> freduce -> withVisible -> <Anonymous>
Execution halted
Package required but not available: ‘revdbayes’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘RTisean’ ‘tsDyn’ ‘forecast’
Error in re-building vignettes:
  ...
Quitting from lines 17-33 (Discriminability.Rmd) 
Error: processing vignette ‘Discriminability.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘dplyr’

Package suggested but not available for checking: ‘grasp2db’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qdap’
Error in re-building vignettes:
  ...
Quitting from lines 95-96 (Safe-Substitution.Rmd) 
Error: processing vignette ‘Safe-Substitution.Rmd’ failed with diagnostics:
there is no package called 'qdap'
Execution halted
Package suggested but not available for checking: ‘structSSI’
Package required but not available: ‘mice’

Packages suggested but not available for checking:
  ‘BIFIEsurvey’ ‘car’ ‘haven’ ‘mitml’ ‘sjlabelled’

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

Package suggested but not available for checking: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘systemfit’
Packages suggested but not available for checking:
  ‘mice’ ‘dplyr’ ‘broom’ ‘car’
Error in re-building vignettes:
  ...
Quitting from lines 194-221 (miceFast-intro.Rmd) 
Error: processing vignette ‘miceFast-intro.Rmd’ failed with diagnostics:
there is no package called 'mice'
Execution halted
Package required but not available: ‘mice’

Package suggested but not available for checking: ‘VIM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mice’ ‘GJRM’ ‘sampleSelection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘broom’ ‘dplyr’ ‘mitml’

Packages suggested but not available for checking:
  ‘CALIBERrfimpute’ ‘Zelig’ ‘micemd’ ‘miceadds’ ‘tidyr’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [10s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2016 Nuno Fachada
  > # Distributed under the MIT License (http://opensource.org/licenses/MIT)
  > 
  > library(testthat)
  > 
  > test_check("micompr")
  Loading required package: micompr
  ── 1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R
  subscript out of bounds
  1: assumptions(cmp) at testthat/test_cmpoutput.R:214
  2: assumptions.cmpoutput(cmp)
  
  ── 2. Error: micomp assumptions have the correct properties (@test_micomp.R#281)
  subscript out of bounds
  1: assumptions(mic1a) at testthat/test_micomp.R:281
  2: assumptions.micomp(mic1a)
  3: lapply(obj, function(x) assumptions(x))
  4: FUN(X[[i]], ...)
  5: assumptions(x)
  6: assumptions.cmpoutput(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 363 SKIPPED: 0 FAILED: 2
  1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R#214) 
  2. Error: micomp assumptions have the correct properties (@test_micomp.R#281) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette ‘paper.Rnw’ failed with diagnostics:
subscript out of bounds
Execution halted
Packages required but not available: ‘Hmisc’ ‘HH’ ‘ggplot2’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘readr’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘midastouch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mice.impute.midastouch
> ### Title: Predictive Mean Matching with distance aided selection of donors
> ### Aliases: mice.impute.midastouch midastouch
> ### Keywords: mice
> 
> ### ** Examples
> 
> ## from R:: mice, slightly adapted ##
> 
> # do default multiple imputation on a numeric matrix
> library(midastouch)
> library(mice)
Error in library(mice) : there is no package called ‘mice’
Execution halted
Error in re-building vignettes:
  ...
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.4657.
trying URL ‘http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz’
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Quitting from lines 634-643 (milr-intro.Rmd) 
Error: processing vignette ‘milr-intro.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘testthis’
Packages required but not available: ‘ggplot2’ ‘dendextend’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘misc3d-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contour3d
> ### Title: Draw an Isosurface, a Three Dimension Contour Plot
> ### Aliases: contour3d
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   #Example 1: Draw a ball
>   f <- function(x, y, z)x^2+y^2+z^2
>   x <- seq(-2,2,len=20)
>   contour3d(f,4,x,x,x)
Error in loadRGL() : rgl is mot available
Calls: contour3d -> drawScene.rgl -> loadRGL
Execution halted
Packages required but not available: ‘ggplot2’ ‘GGally’

Packages suggested but not available for checking: ‘Hmisc’ ‘mice’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘car’ ‘ggplot2’
Package required but not available: ‘haven’

Packages suggested but not available for checking: ‘mice’ ‘miceadds’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘tibble’ ‘purrr’ ‘dplyr’ ‘ggplot2’ ‘tidyr’
Running examples in ‘mixdir-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_features
> ### Title: Plot cluster distribution for a subset of features features
> ### Aliases: plot_features
> 
> ### ** Examples
> 
>   data("mushroom")
>   res <- mixdir(mushroom[1:100, ], n_latent=4)
>   plot_features(c("bruises", "edible"), res$category_prob)
Loading required namespace: ggplot2
Failed with error:  ‘there is no package called ‘ggplot2’’
Loading required namespace: dplyr
Failed with error:  ‘there is no package called ‘dplyr’’
Loading required namespace: tibble
Failed with error:  ‘there is no package called ‘tibble’’
Loading required namespace: purrr
Failed with error:  ‘there is no package called ‘purrr’’
Loading required namespace: tidyr
Failed with error:  ‘there is no package called ‘tidyr’’
Error in plot_features(c("bruises", "edible"), res$category_prob) : 
  This method requires the package: ggplot2,dplyr,tibble,purrr,tidyr. Please install it and try again
Execution halted
Packages required but not available: ‘mixOmics’ ‘ggplot2’ ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘rgl’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Package 'mclust' version 5.4
Type 'citation("mclust")' for citing this R package in publications.
mixpack: a package for mixture components analysis
Quitting from lines 17-21 (mixture_components.Rmd) 
Error: processing vignette ‘mixture_components.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggmcmc’ ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’

Packages suggested but not available for checking:
  ‘pitchRx’ ‘viridis’ ‘ggplot2’ ‘plotly’ ‘dbplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘sparklyr’ ‘purrr’ ‘tibble’

Packages suggested but not available for checking: ‘ggplot2’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘minfi’ ‘GEOquery’
Error in re-building vignettes:
  ...
Quitting from lines 73-76 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'minfi'
Execution halted
Packages suggested but not available for checking: ‘car’ ‘AER’ ‘ggplot2’
Running examples in ‘mlogit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hmftest
> ### Title: Hausman-McFadden Test
> ### Aliases: hmftest hmftest.formula hmftest.mlogit
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> ## from Greene's Econometric Analysis p. 731
> 
> 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
Running ‘AER.R’ [0s/1s]
Running the tests in ‘tests/AER.R’ failed.
Complete output:
  > data("BankWages", package = "AER")
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'AER'
  Calls: data -> find.package
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: Formula
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Quitting from lines 249-251 (mlogit.rnw) 
Error: processing vignette ‘mlogit.rnw’ failed with diagnostics:
there is no package called 'AER'
Execution halted
Package required but not available: ‘mlr’

Package suggested but not available for checking: ‘Hmisc’

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

Packages suggested but not available for checking:
  ‘cmaesr’ ‘ggplot2’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘adabag’ ‘bartMachine’ ‘caret’ ‘clusterSim’ ‘crs’ ‘elmNN’ ‘Hmisc’
  ‘klaR’ ‘mlrMBO’ ‘refund’ ‘rrlda’ ‘smoof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dynsurv’ ‘AER’
Error in re-building vignettes:
  ...
Loading required package: basefun
Loading required package: variables
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/

Attaching package: 'flexsurv'

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

    Hgompertz, Hllogis, Hlnorm, Hweibull, dgompertz, dllogis,
    hgompertz, hllogis, hlnorm, hweibull, pgompertz, pllogis,
    qgompertz, qllogis, rgompertz, rllogis


Attaching package: 'grid'

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

    unit

Loading required package: RColorBrewer
Loading required package: mvtnorm
Loading required package: TH.data

Attaching package: 'TH.data'

The following object is masked from 'package:HSAUR3':

    birds

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

    geyser

trying URL ‘https://zenodo.org/record/17179/files/DVC.tgz’
Content type 'application/octet-stream' length 2292581 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

Quitting from lines 1213-1219 (mlt.Rnw) 
Error: processing vignette ‘mlt.Rnw’ failed with diagnostics:
there is no package called 'AER'
Execution halted
Packages required but not available: ‘qgraph’ ‘dplyr’ ‘MplusAutomation’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘cowplot’ ‘ggplot2’ ‘tidyr’
Error in re-building vignettes:
  ...
Quitting from lines 304-389 (modcmfitrOverview.Rmd) 
Error: processing vignette ‘modcmfitrOverview.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggbeeswarm’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’ ‘ggplot2’ ‘readr’

Packages suggested but not available for checking:
  ‘dbplyr’ ‘nycflights13’ ‘tidypredict’ ‘dbplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ModelGood-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AutoSelectLRM
> ### Title: Automated backward elemination for logistic regression
> ### Aliases: AutoSelectLRM
> 
> ### ** Examples
> 
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Found the following significant warnings:
  confusionMatrix_.cpp:10:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:12:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:14:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:16:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:57:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:104:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:106:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:108:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:110:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ModelMetrics.Rcheck/00install.out’ for details.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘janitor’ ‘broom’

Packages suggested but not available for checking: ‘tidyverse’ ‘ggplot2’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: marg.ivreg
> ### Title: Predicted Margins for 'ivreg' objects from the 'AER' package
> ### Aliases: marg.ivreg
> 
> ### ** Examples
> 
> # From ?AER::ivreg
> 
> # data
> data("CigarettesSW", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Packages suggested but not available for checking: ‘smoof’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 106-114 (Basic_Usage.Rmd) 
Error: processing vignette ‘Basic_Usage.Rmd’ failed with diagnostics:
there is no package called 'smoof'
Execution halted
Package required but not available: ‘tolerance’

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

Package suggested but not available for checking: ‘rglwidget’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘crawl’ ‘ggmap’ ‘ggplot2’ ‘moveHMM’ ‘car’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘geomorph’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘nycflights13’ ‘dbplyr’ ‘dplyr’
Running examples in ‘MonetDBLite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: src_monetdb
> ### Title: dplyr integration from MonetDBLite
> ### Aliases: src_monetdb src_monetdblite
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [13s/61s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > # Sys.setenv("MONETDBLITE_INMEMORY" = "yes")
  > # test_check("MonetDBLite")
  > Sys.setenv("MONETDBLITE_INMEMORY" = "no")
  > test_check("MonetDBLite")
  Loading required package: MonetDBLite
  ── 1. Error: (unknown) (@test_04_dplyr.R#2)  ───────────────────────────────────
  there is no package called 'dplyr'
  1: library(dplyr) at testthat/test_04_dplyr.R:2
  2: stop(txt, domain = NA)
  
  [1] "E"
  [1] "H"
  [1] "M"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 279 SKIPPED: 10 FAILED: 1
  1. Error: (unknown) (@test_04_dplyr.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘dplyr’
Package required but not available: ‘sitar’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 316-320 (MonteCarlo-Vignette.Rmd) 
Error: processing vignette ‘MonteCarlo-Vignette.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Running examples in ‘moonBook-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rank2group
> ### Title: rank a numeric vector and returns a new ordinal vector
> ### Aliases: rank2group
> 
> ### ** Examples
> 
> 
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> data(diamonds)
Warning in data(diamonds) : data set ‘diamonds’ not found
> diamonds$PriceGroup=rank2group(diamonds$price,4)
Error in rank2group(diamonds$price, 4) : object 'diamonds' not found
Execution halted
Package required but not available: ‘rgl’

Packages suggested but not available for checking: ‘car’ ‘shapes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘tidyr’ ‘dplyr’ ‘ggplot2’
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mortAAR)
  > 
  > test_check("mortAAR")
  ── 1. Error: life.table does the mathing correctly (@test_analytical_functions_c
  there is no package called 'dplyr'
  1: expect_true(dplyr::near(single_life_table$dx, schleswig_ma$dx/10, tol = 0.1) %>% 
         all) at testthat/test_analytical_functions_calculations.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: dplyr::near(single_life_table$dx, schleswig_ma$dx/10, tol = 0.1) %>% all
  5: eval(lhs, parent, parent)
  6: eval(lhs, parent, parent)
  7: dplyr::near
  8: getExportedValue(pkg, name)
  9: asNamespace(ns)
  10: getNamespace(ns)
  11: tryCatch(loadNamespace(name), error = function(e) stop(e))
  12: tryCatchList(expr, classes, parentenv, handlers)
  13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  14: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 81 SKIPPED: 0 FAILED: 1
  1. Error: life.table does the mathing correctly (@test_analytical_functions_calculations.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: bitops
Quitting from lines 63-65 (mortAAR_vignette-1.Rmd) 
Error: processing vignette ‘mortAAR_vignette-1.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘mosaicCore’ ‘mosaic’

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

Packages suggested but not available for checking: ‘mosaic’ ‘ggformula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘mosaic’ ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘ggformula’
Packages required but not available:
  ‘mosaicCore’ ‘dplyr’ ‘caret’ ‘ggplot2’ ‘ggformula’ ‘tibble’ ‘tidyr’
  ‘tidyverse’

Package suggested but not available for checking: ‘mosaic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggformula’ ‘mosaicCore’ ‘ggplot2’ ‘tidyr’ ‘readr’ ‘ggdendro’
  ‘broom’

Packages suggested but not available for checking: ‘fastR’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: geosphere
Loading required package: sp
Loading required package: raster
Loading required package: rgdal
rgdal: version: 1.3-3, (SVN revision 759)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.3.0, released 2018/05/04
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.1.0, June 1st, 2018, [PJ_VERSION: 510]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-1 
Warning in .local(x, y, time, data, proj, ...) :
  There were NA locations detected and omitted. Currently they are not stored in unusedrecords
Loading required package: ggmap
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggmap’
Loading required package: mapproj
Loading required package: maps

Error: processing vignette ‘move.Rnw’ failed with diagnostics:
 chunk 15 (label = googleplot) 
Error in ggmap(m) : could not find function "ggmap"
Execution halted
Packages required but not available: ‘ggplot2’ ‘RStoolbox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘matlib’
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking: ‘mvoutlier’ ‘DT’

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

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

Packages suggested but not available for checking: ‘geojsonio’ ‘rmapshaper’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘mrMLM’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘hydroPSO’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mscstexta4r’
Package required but not available: ‘xcms’

Depends: includes the non-default packages:
  ‘amap’ ‘clValid’ ‘cluster’ ‘fpc’ ‘mzR’ ‘xcms’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

Package suggested but not available for checking: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rgl’ ‘ggplot2’
Running examples in ‘MSG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: canabalt
> ### Title: The scores of the game Canabalt from Twitter
> ### Aliases: canabalt
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘poio’ ‘tibble’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘car’
Running examples in ‘mthapower-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mthapower
> ### Title: Post-hoc power calculations - mtDNA haplogroups
> ### Aliases: mthapower
> 
> ### ** Examples
> 
> # Example 1:
> pow <- mthapower(n.cases=203, p0=0.443, Nh=13, OR.cas.ctrl=2.33, sig.level=0.05)
> 
> # Example 2:
> # Create data frames
> pow.H150 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.5, sig.level=0.05)
> pow.H175 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.75, sig.level=0.05)
> pow.H200 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2, sig.level=0.05)
> pow.H250 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2.5, sig.level=0.05)
> 
> # Bind the three data frames:
> bindata <- rbind(pow.H150,pow.H175,pow.H200,pow.H250)
> # Adds column OR to binded data frame:
> bindata$OR <- rep(factor(c(1.50,1.75,2,2.5)),
+               times = c(nrow(pow.H150),
+                         nrow(pow.H175),
+                         nrow(pow.H200),
+                         nrow(pow.H250)))
> # Create plot:
> # install.packages("car")
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tibble’ ‘readr’ ‘tidyr’ ‘tidyselect’

Package suggested but not available for checking: ‘dbplyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Error: processing vignette ‘chfls1.Rnw’ failed with diagnostics:
 chunk 1 (label = setup) 
Error in library("car") : there is no package called ‘car’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 121-130 (SIR-MCMC.Rmd) 
Error: processing vignette ‘SIR-MCMC.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘tidyverse’

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

Depends: includes the non-default packages:
  ‘car’ ‘pdist’ ‘pls’ ‘gplots’ ‘mvtnorm’ ‘robustbase’ ‘gtools’ ‘bitops’
  ‘caTools’ ‘pcaPP’ ‘rrcov’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  ‘cplm’ ‘logistf’
Running examples in ‘munsell-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chroma_slice
> ### Title: Plot all colours with the same chroma
> ### Aliases: chroma_slice
> 
> ### ** Examples
> 
> chroma_slice(2)
Error: ggplot2 needed for this function to work. Please install it.
Execution halted
Running examples in ‘musica-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare
> ### Title: Compare decomposed variables
> ### Aliases: compare
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 17-20 (using_musica.Rmd) 
Error: processing vignette ‘using_musica.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘mutoss-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Qvalue
> ### Title: Storey's (2001) q-value Procedure...
> ### Aliases: Qvalue
> 
> ### ** Examples
> pval <- c(runif(50), runif(50, 0, 0.01))
> result <- Qvalue(pval)
Loading required package: qvalue
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘qvalue’
Package qvalue is required - should we install it?
Error in requireLibrary("qvalue") : 
  Required package qvalue should not be installed
Calls: Qvalue -> requireLibrary
Execution halted
Package required but not available: ‘rattle’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: phytools
Loading required package: ape
Loading required package: maps
Loading required package: corpcor
Loading required package: subplex
##
## mvMORPH package (1.0.9)
## Multivariate evolutionary models
##
## See the tutorials: browseVignettes("mvMORPH")
##
## To cite package 'mvMORPH': citation("mvMORPH")
##
Done.
Efficient parameterization is not yet implemented for user-defined constraints
Please check the results carefully!!
Efficient parameterization is not yet implemented for user-defined constraints
Please check the results carefully!!
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Done.
Quitting from lines 326-349 (tutorial_mvMORPH.Rmd) 
Error: processing vignette ‘tutorial_mvMORPH.Rmd’ failed with diagnostics:
could not find function "ellipse"
Execution halted
Packages required but not available: ‘mvoutlier’ ‘kableExtra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘mvQuad-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot (plot.NIGrid)
> ### Title: plots an NIGrid-object
> ### Aliases: 'plot (plot.NIGrid)' plot.NIGrid
> 
> ### ** Examples
> 
> myGrid <- createNIGrid(dim=4, type=c("GHe", "cNC1", "GLe", "oNC1"),
+                        level=c(3,4,5,6))
> plot(myGrid) ## dimension 1-min(3,dim(myGrid)) are plotted
Error in plot.NIGrid(myGrid) : 
  wrong dimensions stated to be plotted (no 'rgl'-package for 3d-plot)
Calls: plot -> plot.NIGrid
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 31-43 (mvtboost_vignette.Rmd) 
Error: processing vignette ‘mvtboost_vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘mwaved-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiWaveD
> ### Title: Full mWaveD analysis
> ### Aliases: multiWaveD
> 
> ### ** Examples
> 
> library(mwaved)
> # Simulate the multichannel doppler signal.
> m <- 3
> n <- 2^10
> signal <- makeDoppler(n)
> # Noise levels per channel
> e <- rnorm(m * n)
> # Create Gamma blur
> shape <- seq(from = 0.5, to = 1, length = m)
> scale <- rep(0.25, m)
> G <- gammaBlur(n, shape = shape, scale = scale)
> # Convolve the signal
> X <- blurSignal(signal, G)
> # Create error with custom signal to noise ratio
> SNR <- c(10, 15, 20)
> sigma <- sigmaSNR(X, SNR)
> if (requireNamespace("fracdiff", quietly = TRUE)) {
+   alpha <- c(0.75, 0.8, 1)
+ } else {
+   alpha <- rep(1, m)
+ }
> E <- multiNoise(n, sigma, alpha)
> # Create noisy & blurred multichannel signal
> Y <- X + E
> # Compute mWaveD object
> mWaveDObj <- multiWaveD(Y, G = G, alpha = alpha)
> plot(mWaveDObj)
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: plot ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 14-53 (mWaveD.Rmd) 
Error: processing vignette ‘mWaveD.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘biomartr’ ‘dplyr’ ‘taxize’ ‘ggplot2’ ‘readr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘filesstrings’ ‘autothresholdr’ ‘dplyr’ ‘purrr’ ‘detrendr’ ‘ijtiff’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tidyr’ ‘tibble’ ‘visdat’ ‘forcats’
  ‘viridis’

Packages suggested but not available for checking:
  ‘wakefield’ ‘vdiffr’ ‘imputeTS’ ‘UpSetR’

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

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

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

Package suggested but not available for checking: ‘rglwidget’

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

Package suggested but not available for checking: ‘alphashape3d’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘heatmaply’ ‘ggplot2’ ‘dendextend’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘car’ ‘Hmisc’ ‘quickPlot’ ‘SpaDES.tools’

Packages suggested but not available for checking: ‘fastshp’ ‘SpaDES.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘netrankr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_rank_intervals
> ### Title: Plot rank intervals
> ### Aliases: plot_rank_intervals
> 
> ### ** 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(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Quitting from lines 70-71 (partial_centrality.Rmd) 
Error: processing vignette ‘partial_centrality.Rmd’ failed with diagnostics:
ggplot2 needed for this function to work. Please install it.
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggvis’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘broom’ ‘dplyr’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggrepel’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘surveybootstrap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘qgraph’ ‘IsingFit’ ‘ggplot2’ ‘NetworkComparisonTest’ ‘smacof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tidyr’

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 11-19 (nifti_basics.Rmd) 
Error: processing vignette ‘nifti_basics.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 15-18 (hcp.Rmd) 
Error: processing vignette ‘hcp.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘readr’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyverse’ ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘ggcorrplot’ ‘Hmisc’ ‘caret’

Package suggested but not available for checking: ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘ggpmisc’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘NFPdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggthemes’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘rstan’ ‘ggplot2’ ‘tensorflow’
Package required but not available: ‘tibble’

Packages which this enhances but not available for checking:
  ‘kokudosuuchi’ ‘estatapi’ ‘jpndistrict’ ‘jpmesh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘vpc’

Package suggested but not available for checking: ‘dplyr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘dplyr’ ‘tidyr’ ‘tibble’

Packages suggested but not available for checking: ‘ggplot2’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘broom’ ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘Hmisc’
Running examples in ‘nLTT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_nltt_values
> ### Title: Collects the nLTT values of all phylogenies in the
> ###   melted/uncast/long form
> ### Aliases: get_nltt_values
> 
> ### ** Examples
> 
>   library(ape)
>   library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 60-65 (get_nltt_values.Rmd) 
Error: processing vignette ‘get_nltt_values.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘d3heatmap’ ‘tidyr’

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

Package suggested but not available for checking: ‘thief’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘choroplethr’ ‘dplyr’ ‘forcats’ ‘ggplot2’ ‘hurricaneexposure’ ‘tidyr’
  ‘viridis’

Packages suggested but not available for checking:
  ‘hurricaneexposuredata’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyr’ ‘dplyr’ ‘ggplot2’ ‘ggmap’ ‘ggExtra’ ‘tcR’

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

Packages suggested but not available for checking: ‘purrr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘metaplot’

Package suggested but not available for checking: ‘wrangle’

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

Depends: includes the non-default packages:
  ‘lpSolve’ ‘gdata’ ‘Hmisc’ ‘rms’ ‘geometry’ ‘psych’ ‘pwt’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘plotly’ ‘ggplot2’ ‘GGally’

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

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

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

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

Packages suggested but not available for checking: ‘dbplyr’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘ggthemes’ ‘GGally’ ‘forcats’
Running examples in ‘nzelect-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GE2014
> ### Title: General Election Results 2014
> ### Aliases: GE2014
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # the following matches the results published at
> # http://www.electionresults.govt.nz/electionresults_2014/e9/html/e9_part1.html
> library(tidyr)
Error in library(tidyr) : there is no package called ‘tidyr’
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(nzelect)
  > 
  > test_check("nzelect")
  ── 1. Error: (unknown) (@test_totals_v_published2014.R#8)  ─────────────────────
  object 'Party' not found
  1: expect_equal(sum(filter(GE2014, Party == "National Party" & VotingType == "Party")$Votes), 
         1131501) at testthat/test_totals_v_published2014.R:8
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: filter(GE2014, Party == "National Party" & VotingType == "Party")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 7 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_totals_v_published2014.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘AGread’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘plot3Drgl’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘marmap’
Packages suggested but not available for checking: ‘tibble’ ‘ggplot2’
Packages required but not available:
  ‘car’ ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘recipes’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘caret’ ‘descriptr’ ‘haven’ ‘readr’ ‘readxl’ ‘vdiffr’

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

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

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘haven’ ‘feather’
Package required but not available: ‘mlr’

Package suggested but not available for checking: ‘farff’

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

Packages suggested but not available for checking:
  ‘readr’ ‘tibble’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘InSilicoVA’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: nlme
This is mgcv 1.8-24. For overview type 'help("mgcv-package")'.
Quitting from lines 92-96 (opera-vignette.Rmd) 
Error: processing vignette ‘opera-vignette.Rmd’ failed with diagnostics:
there is no package called 'caret'
Execution halted
Package required but not available: ‘DepthProc’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘caret’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 84-103 (ordinalClust.Rmd) 
Error: processing vignette ‘ordinalClust.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running ‘testthat.R’ [11s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(origami)
  origami: Generalized Cross-Validation Framework
  Version: 1.0.0
  > library(data.table)
  > test_check("origami")
  ── 1. Error: (unknown) (@test-overall_timeseries.R#1)  ─────────────────────────
  there is no package called 'forecast'
  1: library(forecast) at testthat/test-overall_timeseries.R:1
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 24 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-overall_timeseries.R#1) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 286-321 (generalizedCV.Rmd) 
Error: processing vignette ‘generalizedCV.Rmd’ failed with diagnostics:
there is no package called 'forecast'
Execution halted
Package required but not available: ‘OpenStreetMap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘keras’ ‘pROC’
Error in re-building vignettes:
  ...
Loading required package: knitcitations
Loading required package: OSTSC
Loading required package: keras
Loading required package: dummies
dummies-1.5.6 provided by Decision Patterns

Loading required package: pROC
Quitting from lines 518-526 (Over_Sampling_for_Time_Series_Classification.Rmd) 
Error: processing vignette ‘Over_Sampling_for_Time_Series_Classification.Rmd’ failed with diagnostics:
there is no package called 'pROC'
Execution halted
Package required but not available: ‘reldist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘forcats’ ‘HDoutliers’ ‘cellWise’ ‘GGally’

Package suggested but not available for checking: ‘mbgraphic’

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

Package suggested but not available for checking: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggiraph’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 98-112 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘pagenum-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pagenum
> ### Title: Put Page Numbers on Graphics
> ### Aliases: pagenum setPagenum getPagenum setPagenum getPagenum
> 
> ### ** Examples
> 
> # base graphics
> setPagenum(1)
> plot(Sepal.Length~Sepal.Width, data=iris, col=Species, pch=19)
> pagenum()
> 
> # lattice, date
> setPagenum(getPagenum()+1) # Manual increment
> require(lattice)
Loading required package: lattice
> xyplot(Sepal.Length~Sepal.Width, data=iris, groups=Species)
> pagenum(date=TRUE)
> 
> # ggplot2, top-right
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> ggplot(iris, aes(x=Sepal.Width, y=Sepal.Length,
+   color=Species)) + geom_point() + theme_classic()
Error in ggplot(iris, aes(x = Sepal.Width, y = Sepal.Length, color = Species)) : 
  could not find function "ggplot"
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pagenum)
  > 
  > test_check("pagenum")
  ── 1. Error: (unknown) (@test_pagenum.R#17)  ───────────────────────────────────
  could not find function "ggplot"
  1: .handleSimpleError(function (e) 
     {
         handled <<- TRUE
         test_error <<- e
         options(expressions = expressions_opt_new)
         on.exit(options(expressions = expressions_opt), add = TRUE)
         e$expectation_calls <- frame_calls(11, 2)
         test_error <<- e
         register_expectation(e)
         e$handled <- TRUE
         test_error <<- e
     }, "could not find function \"ggplot\"", quote(ggplot(iris, aes(x = Sepal.Width, 
         y = Sepal.Length, color = Species)))) at testthat/test_pagenum.R:17
  2: eval(code, test_env)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_pagenum.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 74-79 (pagenum_examples.Rmd) 
Error: processing vignette ‘pagenum_examples.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘mcprofile’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘agricolae’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘paleomorph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSpecimens
> ### Title: Plot an array of specimen landmark data in an interactive 3D
> ###   frame
> ### Aliases: plotSpecimens
> 
> ### ** Examples
> 
> A <- array(rep(rnorm(3 * 20, sd = 30), by = 6) + rnorm(6 * 20 * 3), 
+        dim = c(20, 3, 6))
> plotSpecimens(A)
Error: Package rgl needed for this function to work. Please install it with install.packages('rgl').
Execution halted
Running examples in ‘palettetown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_colour_poke
> ### Title: Add a pokemon palette to a ggplot2 colour or fill scale.
> ### Aliases: scale_color_poke scale_colour_poke scale_fill_poke
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘FactoClass’

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

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘tables’ ‘rms’ ‘forecast’
Error in re-building vignettes:
  ...
Quitting from lines 13-18 (pander.Rmd) 
Error: processing vignette ‘pander.Rmd’ failed with diagnostics:
there is no package called 'tables'
Execution halted
Packages required but not available: ‘oai’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘parallelDist.Rnw’ failed with diagnostics:
 chunk 2 (label = performanceDtw) 
Error in ggplot(data = comparison, aes(x = expr, y = min, group = method,  : 
  could not find function "ggplot"
Execution halted
Packages suggested but not available for checking: ‘GGally’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 26-34 (Simulating-Power.Rmd) 
Error: processing vignette ‘Simulating-Power.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘hansard’ ‘mnis’ ‘dplyr’ ‘tibble’

Packages suggested but not available for checking: ‘leaflet’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘dbplyr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘PartCensReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cens.SMN.PCR
> ### Title: Estimation and diagnostics for partially linear censored
> ###   regression models
> ### Aliases: Cens.SMN.PCR
> ### Keywords: package censored censoring diagnostic partial partially
> 
> ### ** Examples
> 
> dtawage = get(data(PSID1976,package = "AER"))
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: get -> data -> find.package
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘egcm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘partialAR’ ‘ggplot2’

Package suggested but not available for checking: ‘egcm’

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

Package suggested but not available for checking: ‘ggraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: RWeka
Loading required namespace: XML
Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

Loading required package: coin
Loading required package: survival

Attaching package: ‘survival’

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

    solder

Loading required package: strucchange
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: Formula
Loading required package: modeltools
Loading required package: stats4

Attaching package: ‘party’

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

    cforest, ctree, ctree_control, edge_simple, mob,
    mob_control, node_barplot, node_bivplot, node_boxplot,
    node_inner, node_surv, node_terminal, varimp

Loading required namespace: vcd

Error: processing vignette ‘mob.Rnw’ failed with diagnostics:
 chunk 26 (label = Journals-data) 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Execution halted
Packages suggested but not available for checking:
  ‘DT’ ‘ggplot2’ ‘tidyverse’ ‘gapminder’
Error in re-building vignettes:
  ...
Quitting from lines 32-39 (passport.Rmd) 
Error: processing vignette ‘passport.Rmd’ failed with diagnostics:
there is no package called 'gapminder'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 209-220 (getting-started.Rmd) 
Error: processing vignette ‘getting-started.Rmd’ failed with diagnostics:
there is no package called 'tidyr'
Execution halted
Packages required but not available: ‘mice’ ‘MplusAutomation’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘PBImisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flu
> ### Title: Numbers of flu occurences in the 10 years period in the Poland.
> ### Aliases: flu
> ### Keywords: flu
> 
> ### ** Examples
> 
> data(flu)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘phylosim’

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

Packages suggested but not available for checking: ‘dplyr’ ‘RDML’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘purrr’ ‘readr’ ‘ggplot2’ ‘broom’

Package suggested but not available for checking: ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘strvalidator’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

Packages suggested but not available for checking: ‘adabag’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <rsnak>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <testit>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 734-750 (PDQutils.Rnw) 
Error: processing vignette ‘PDQutils.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘car’ ‘coefplot’ ‘papeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘viridis’ ‘ggthemes’
Running examples in ‘PeakError-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PeakError
> ### Title: PeakError
> ### Aliases: PeakError
> 
> ### ** Examples
> 
> x <- seq(5, 85, by=5)
> peaks <- rbind(Peaks("chr2", x, x+3),
+                Peaks("chr3", c(25, 38, 57), c(33, 54, 75)),
+                Peaks("chr4", c(5, 32, 38, 65), c(15, 35, 55, 85)),
+                Peaks("chr5", c(12, 26, 56, 75), c(16, 54, 59, 85)))
> regions <- NULL
> for(chr in 1:5){
+   regions <- rbind(regions, {
+     data.frame(chrom=paste0("chr", chr),
+                chromStart=c(10, 30, 50, 70),
+                chromEnd=c(20, 40, 60, 80),
+                annotation=c("noPeaks", "peakStart", "peakEnd", "peaks"))
+   })
+ }
> err <- PeakError(peaks, regions)
> ann.colors <-
+   c(noPeaks="#f6f4bf",
+     peakStart="#ffafaf",
+     peakEnd="#ff4c4c",
+     peaks="#a445ee")
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘penaltyLearning’
Running examples in ‘PeakSegDP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chr11ChIPseq
> ### Title: ChIP-seq aligned read coverage for 4 samples on a subset of
> ###   chr11
> ### Aliases: chr11ChIPseq
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(chr11ChIPseq)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘penaltyLearning’

Package suggested but not available for checking: ‘ggplot2’

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

Packages suggested but not available for checking: ‘riskRegression’ ‘Hmisc’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotHD
> ### Title: Histogram and density plot
> ### Aliases: plotHD
> ### Keywords: dplot
> 
> ### ** Examples
> 
> x <- rnorm(100, 10, 2)
> plotHD(x, HD = "stack")
Error: Package 'car' needed for this function to work. Please install it.
Execution halted
Package required but not available: ‘adegenet’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘penalizedSVM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict
> ### Title: Predict Method for Feature Selection SVM
> ### Aliases: predict.penSVM
> 
> ### ** Examples
> 
> 
> seed<- 123
> train<-sim.data(n = 200, ng = 100, nsg = 10, corr=FALSE, seed=seed )
> print(str(train)) 
List of 3
 $ x   : num [1:100, 1:200] 0.547 0.635 -0.894 0.786 2.028 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:100] "pos1" "pos2" "pos3" "pos4" ...
  .. ..$ : chr [1:200] "1" "2" "3" "4" ...
 $ y   : Named num [1:200] 1 -1 -1 1 -1 -1 1 -1 -1 -1 ...
  ..- attr(*, "names")= chr [1:200] "1" "2" "3" "4" ...
 $ seed: num 123
NULL
> 
> #train standard svm
> my.svm<-svm(x=t(train$x), y=train$y, kernel="linear")
> 
> # test with other data
> test<- sim.data(n = 200, ng = 100, nsg = 10, seed=(seed+1) )
> 
> # Check accuracy standard SVM
> my.pred <-ifelse( predict(my.svm, t(test$x)) >0,1,-1)
> # Check accuracy:
> table(my.pred, test$y)
       
my.pred -1  1
     -1 81 23
     1  30 66
> 
> # define set values of tuning parameter lambda1 for SCAD 
> lambda1.scad <- c (seq(0.01 ,0.05, .01),  seq(0.1,0.5, 0.2), 1 ) 
> # for presentation don't check  all lambdas : time consuming! 
> # computation intensive; for demostration reasons only for the first 100 features
> # and only for 10 Iterations maxIter=10, default maxIter=700
> 
> system.time(fit.scad<- svm.fs(x=t(train$x)[,1:100],y=train$y, fs.method="scad", cross.outer= 0,
+ 	grid.search = "discrete",  lambda1.set=lambda1.scad[1:3], show="none",
+ 	parms.coding = "none", maxIter=10,
+ 	inner.val.method = "cv", cross.inner= 5, seed=seed, verbose=FALSE))
Error in UseMethod("svm.fs") : 
  no applicable method for 'svm.fs' applied to an object of class "c('matrix', 'double', 'numeric')"
Calls: system.time -> svm.fs
Timing stopped at: 0 0 0
Execution halted
Package required but not available: ‘pacotest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘tibble’ ‘broom’ ‘tidyr’

Packages suggested but not available for checking: ‘ggplot2’ ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘PerformanceAnalytics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Omega
> ### Title: calculate Omega for a return series
> ### Aliases: Omega
> 
> ### ** Examples
> 
> 
>     data(edhec)
>     Omega(edhec)
               Convertible Arbitrage CTA Global Distressed Securities
Omega (L = 0%)              2.602138   1.936841              3.230443
               Emerging Markets Equity Market Neutral Event Driven
Omega (L = 0%)         1.765435              6.213714     2.999655
               Fixed Income Arbitrage Global Macro Long/Short Equity
Omega (L = 0%)               2.585943     3.516616          2.438064
               Merger Arbitrage Relative Value Short Selling Funds of Funds
Omega (L = 0%)         4.595886       3.815368      1.228785       2.460153
>     Omega(edhec[,13],method="interp",output="point")
Error in FUN(newX[, i], ...) : 
  requireNamespace("Hmisc", quietly = TRUE) is not TRUE
Calls: Omega -> apply -> FUN -> stopifnot
Execution halted
Error in re-building vignettes:
  ...
Loading required package: xts
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric


Attaching package: ‘PerformanceAnalytics’

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

    legend


Attaching package: ‘gplots’

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

    textplot

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

    lowess


Error: processing vignette ‘textplotPresentation-CRUG-2011.Rnw’ failed with diagnostics:
 chunk 5 (label = Hmiscformat) 
Error in library(Hmisc) : there is no package called ‘Hmisc’
Execution halted
Packages required but not available: ‘ggplot2’ ‘tidyr’ ‘dplyr’

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

Packages suggested but not available for checking:
  ‘dendextend’ ‘dendextendRcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

Packages suggested but not available for checking: ‘dplyr’ ‘tidyr’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: perturb
> ### Title: Perturbation analysis to evaluate collinearity
> ### Aliases: perturb summary.perturb print.summary.perturb
> ### Keywords: regression
> 
> ### ** Examples
> 
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Packages required but not available: ‘tibble’ ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘cowplot’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘readr’ ‘ggplot2’
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggspectra’ ‘photobiologyWavebands’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘photobiology’ ‘tibble’ ‘dplyr’ ‘tidyr’ ‘readr’ ‘readxl’ ‘hyperSpec’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggspectra’ ‘photobiologyWavebands’

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

Packages suggested but not available for checking:
  ‘ggspectra’ ‘photobiologyWavebands’ ‘ggplot2’

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

Packages suggested but not available for checking:
  ‘photobiologyWavebands’ ‘ggspectra’ ‘ggplot2’

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

Packages suggested but not available for checking: ‘ggplot2’ ‘ggspectra’

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

Package suggested but not available for checking: ‘ggmap’

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

Packages suggested but not available for checking:
  ‘photobiologyWavebands’ ‘ggplot2’ ‘ggspectra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(phrasemachine)
  phrasemachine: Simple Phrase Extraction
  Version 1.1.2 created on 2017-05-29.
  copyright (c) 2016, Matthew J. Denny, Abram Handler, Brendan O'Connor.
  Type help('phrasemachine') or
  vignette('getting_started_with_phrasemachine') to get started.
  Development website: https://github.com/slanglab/phrasemachine
  > 
  > test_check("phrasemachine")
  ── 1. Error: See if tagging five documents works, and if coarsening works (@test
  there is no package called 'quanteda'
  1: quanteda::data_corpus_inaugural at testthat/test_POS_tag_documents.R:5
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ── 2. Error: See if extractor works (@test_extract_phrases.R#5)  ───────────────
  there is no package called 'quanteda'
  1: quanteda::data_corpus_inaugural at testthat/test_extract_phrases.R:5
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 2
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#5) 
  2. Error: See if extractor works (@test_extract_phrases.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 82-91 (getting_started_with_phrasemachine.Rmd) 
Error: processing vignette ‘getting_started_with_phrasemachine.Rmd’ failed with diagnostics:
there is no package called 'quanteda'
Execution halted
Package suggested but not available for checking: ‘OutbreakTools’
Package required but not available: ‘RNeXML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘drc’ ‘geomorph’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rphylopars’
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘ggraph’ ‘purrr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘phyloseq’ ‘ggnetwork’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 16-43 (IdealWeightComparison.Rmd) 
Error: processing vignette ‘IdealWeightComparison.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘tibble’

Packages suggested but not available for checking:
  ‘tidyverse’ ‘pinnacle.API’ ‘Lahman’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘modelr’ ‘tidyverse’
Error in re-building vignettes:
  ...
Quitting from lines 119-141 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘dplyr’ ‘ggsubplot’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘dbplyr’ ‘purrr’ ‘tidyselect’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘broom’ ‘dplyr’ ‘tidyr’

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

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggnetwork’ ‘ggplot2’ ‘dplyr’ ‘tibble’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Depends: includes the non-default packages:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘lattice’ ‘rggobi’ ‘ggplot2’
  ‘proto’
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: ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking: ‘cowplot’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘readr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘BradleyTerryScalable’ ‘StatRank’ ‘kableExtra’ ‘tibble’
Packages required but not available: ‘dplyr’ ‘ggdendro’ ‘ggplot2’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘latticist’ ‘ggplot2’
Packages required but not available: ‘dplyr’ ‘dbplyr’ ‘gistr’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vcovBK
> ### Title: Beck and Katz Robust Covariance Matrix Estimators
> ### Aliases: vcovBK vcovBK.plm
> ### Keywords: regression
> 
> ### ** Examples
> 
> library(lmtest)
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Formula
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Error: processing vignette ‘plm.rnw’ failed with diagnostics:
 chunk 46 
Error in library("car") : there is no package called 'car'
Execution halted
Package required but not available: ‘aqp’

Packages suggested but not available for checking:
  ‘adehabitat’ ‘spcosa’ ‘rgbif’ ‘Hmisc’ ‘GSIF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘ggplot2’

Package suggested but not available for checking: ‘gapminder’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘plotly’
Packages required but not available:
  ‘ggplot2’ ‘tidyr’ ‘dplyr’ ‘tibble’ ‘crosstalk’ ‘purrr’

Packages suggested but not available for checking:
  ‘ggthemes’ ‘GGally’ ‘broom’ ‘dendextend’ ‘RSelenium’

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.
Packages suggested but not available for checking: ‘mixOmics’ ‘SensoMineR’
Running examples in ‘PLSbiplot1-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Mag.Bmat.plot
> ### Title: Magnitude of the Partial Least Squares Regression (PLSR)
> ###   coefficients matrix
> ### Aliases: Mag.Bmat.plot
> 
> ### ** Examples
> 
> if(require(pls))
+ data(oliveoil, package="pls")
Loading required package: pls

Attaching package: ‘pls’

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

    loadings

> X = as.matrix(oliveoil$chemical, ncol=5)
> dimnames(X) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Acidity","Peroxide","K232","K270","DK")))
> Y = as.matrix(oliveoil$sensory, ncol=6)
> dimnames(Y) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Yellow","Green","Brown","Glossy","Transp","Syrup")))
> Mag.Bmat.plot(X, Y, algorithm=mod.SIMPLS, A=2)
> 
> #nutrimouse data
> if(require(mixOmics))
+ data(nutrimouse, package="mixOmics")
Loading required package: mixOmics
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mixOmics’
> X1 = as.matrix(nutrimouse$lipid, ncol=21)
Error in as.matrix(nutrimouse$lipid, ncol = 21) : 
  object 'nutrimouse' not found
Execution halted
Packages suggested but not available for checking: ‘FactoMineR’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 310-329 (plspm_introduction.Rnw) 
Error: processing vignette ‘plspm_introduction.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘plsRglm’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘coreSim’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’

Packages suggested but not available for checking: ‘DT’ ‘styler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘xpose’ ‘GGally’ ‘PKNCA’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘TripleR’

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

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘quanteda’ ‘ggplot2’

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

Packages suggested but not available for checking:
  ‘dplyr’ ‘ggplot2’ ‘readr’ ‘tidyr’

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

Package suggested but not available for checking: ‘tidytext’

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

Package suggested but not available for checking: ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘ggplot2’

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

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘adegenet’ ‘ggplot2’ ‘pegas’ ‘mmod’ ‘GGally’

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

Package suggested but not available for checking: ‘Lahman’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘adegenet’ ‘ggplot2’ ‘pegas’ ‘dplyr’

Package suggested but not available for checking: ‘cowplot’

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

Package suggested but not available for checking: ‘adegenet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Error: processing vignette ‘burkina-faso-females.Rnw’ failed with diagnostics:
 chunk 1 (label = sweave-setup) 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages suggested but not available for checking: ‘FGN’ ‘forecast’
Package required but not available: ‘PortfolioEffectHFT’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘lmerTest’ ‘ggplot2’ ‘ggsci’ ‘viridis’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  Error in library(dplyr) : there is no package called 'dplyr'
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 197-200 (three-level.Rmd) 
Error: processing vignette ‘three-level.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘factoextra’
Error in re-building vignettes:
  ...
Quitting from lines 45-48 (fcm.Rmd) 
Error: processing vignette ‘fcm.Rmd’ failed with diagnostics:
there is no package called 'factoextra'
Execution halted
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘leaflet’ ‘PakPC2017’ ‘tidyr’ ‘tmap’

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

Packages suggested but not available for checking:
  ‘GGally’ ‘ggplot2’ ‘PPtreeViz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tolerance’ ‘ggplot2’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doBy’
Packages required but not available: ‘precrec’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘tibble’ ‘purrr’

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

Package suggested but not available for checking: ‘ggplot2’

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

Package suggested but not available for checking: ‘GenABEL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  ‘AER’ ‘caret’ ‘sampleSelection’
Packages required but not available: ‘caret’ ‘forecast’ ‘TSPred’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 31-62 (prepplotOverview.Rmd) 
Error: processing vignette ‘prepplotOverview.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Package required but not available: ‘caret’

Packages suggested but not available for checking: ‘ggplot2’ ‘preproviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘caret’

Packages suggested but not available for checking: ‘preprocomb’ ‘preproviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘ggplot2’ ‘ggdendro’

Package suggested but not available for checking: ‘preprocomb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘quanteda’ ‘ggplot2’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 50-91 (interpolation-in-small-samples.Rmd) 
Error: processing vignette ‘interpolation-in-small-samples.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘tibble’

Package suggested but not available for checking: ‘gurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 154-155 (prioritylasso_vignette.Rmd) 
Error: processing vignette ‘prioritylasso_vignette.Rmd’ failed with diagnostics:
there is no package called 'pROC'
Execution halted
Packages required but not available:
  ‘bupaR’ ‘processmapR’ ‘dplyr’ ‘tidyr’ ‘DiagrammeR’

Package suggested but not available for checking: ‘edeaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘bupaR’ ‘edeaR’ ‘DiagrammeR’ ‘ggplot2’ ‘ggthemes’ ‘purrr’
  ‘forcats’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘bupaR’ ‘edeaR’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ProFound-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FPtest
> ### Title: False Positive Reference Data
> ### Aliases: FPtest
> ### Keywords: datasets
> 
> ### ** Examples
> 
> image=readFITS(system.file("extdata", 'VIKING/mystery_VIKING_Z.fits', package="ProFound"))
> profound=profoundProFound(image, magzero=30, rotstats=TRUE)
Error: The imager package is needed for this function to work. Please install it from CRAN.
Execution halted
Packages required but not available: ‘ggplot2’ ‘GeneralizedUmatrix’

Package suggested but not available for checking: ‘DataVisualizations’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘incidence’ ‘ggplot2’

Package suggested but not available for checking: ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘readxl’ ‘tibble’
Packages required but not available: ‘rstan’ ‘rstanarm’ ‘ggplot2’

Package suggested but not available for checking: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘rstan’ ‘tidyr’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘ggdendro’ ‘plotly’ ‘rgl’

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

Error: processing vignette ‘PRROC.Rnw’ failed with diagnostics:
 chunk 47 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘PogromcyDanych’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘Hmisc’ ‘ggplot2’
Running examples in ‘pscl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hurdletest
> ### Title: Testing for the Presence of a Zero Hurdle
> ### Aliases: hurdletest
> ### Keywords: regression
> 
> ### ** Examples
> 
> data("bioChemists", package = "pscl")
> fm <- hurdle(art ~ ., data = bioChemists, dist = "negbin", zero = "negbin")
> hurdletest(fm)
Loading required namespace: car
Failed with error:  ‘there is no package called ‘car’’
Error in hurdletest(fm) : requireNamespace("car") is not TRUE
Calls: hurdletest -> stopifnot
Execution halted
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric


Error: processing vignette ‘countreg.Rnw’ failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("car") : there is no package called ‘car’
Execution halted
Packages required but not available: ‘DataCombine’ ‘rio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 403-408 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘tibble’ ‘ggplot2’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tibble’ ‘ggplot2’ ‘tidyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘tidyr’ ‘purrr’ ‘qgraph’ ‘ggcorrplot’ ‘rstanarm’
  ‘lmerTest’ ‘emmeans’ ‘broom’ ‘tibble’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘likert’
Packages required but not available: ‘ggmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggdendro’ ‘kableExtra’

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

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:
  ‘pec’ ‘riskRegression’ ‘rms’
Running examples in ‘Publish-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: publish.CauseSpecificCox
> ### Title: Tabulizing cause-specific hazard ratio from all causes with
> ###   confidence limits and Wald test p-values.
> ### Aliases: publish.CauseSpecificCox
> 
> ### ** Examples
> 
> library(riskRegression)
Error in library(riskRegression) : 
  there is no package called ‘riskRegression’
Execution halted
Running ‘test-glmSeries.R’ [2s/3s]
  Running ‘test-publish-gls.R’ [3s/5s]
  Running ‘test-publish-mi.R’ [2s/3s]
Running the tests in ‘tests/test-publish-mi.R’ failed.
Complete output:
  > library(testthat)
  > library(Publish)
  Loading required package: prodlim
  > library(mitools)
  > library(smcfcs)
  > library(riskRegression)
  Error in library(riskRegression) : 
    there is no package called 'riskRegression'
  Execution halted
Packages required but not available:
  ‘dplyr’ ‘MazamaSpatialUtils’ ‘ggmap’ ‘leaflet’ ‘openair’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘gender’ ‘ggplot2’ ‘tidyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’

Package suggested but not available for checking: ‘tidyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cowplot’ ‘ggplot2’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Packages required but not available: ‘readr’ ‘sjlabelled’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘GGally’ ‘DT’
Error in re-building vignettes:
  ...
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette ‘wilcox1973.Rmd’ failed with diagnostics:
there is no package called 'DT'
Execution halted
Packages required but not available:
  ‘caret’ ‘dplyr’ ‘ggplot2’ ‘ggrepel’ ‘readr’ ‘pROC’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggrepel’

Packages suggested but not available for checking:
  ‘dplyr’ ‘DT’ ‘purrr’ ‘stm’ ‘tibble’ ‘tidytext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘GGally’ ‘ggplot2’ ‘rgl’
Running examples in ‘QuantNorm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: connection.matrix
> ### Title: Construct connection matrix for network analysis
> ### Aliases: connection.matrix
> 
> ### ** Examples
> 
> 
> library(network); library(ggplot2); library(sna); library(GGally) #drawing network graph
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.

Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘labelled’

Packages suggested but not available for checking: ‘dplyr’ ‘forcats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘fastshp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’

Package suggested but not available for checking: ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘ggplot2’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’

Package suggested but not available for checking: ‘data.tree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 106-111 (R2admb.Rnw) 
Error: processing vignette ‘R2admb.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘lmerTest’ ‘ggplot2’ ‘afex’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘doBy’ ‘car’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 78-88 (Performance.Rmd) 
Error: processing vignette ‘Performance.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 28-32 (preparingData.Rmd) 
Error: processing vignette ‘preparingData.Rmd’ failed with diagnostics:
there is no package called 'tidyr'
Execution halted
Packages required but not available:
  ‘radiant.data’ ‘ggplot2’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘tidyr’ ‘dplyr’ ‘tibble’ ‘broom’ ‘car’ ‘DT’ ‘readr’
  ‘readxl’ ‘plotly’

Package suggested but not available for checking: ‘feather’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘radiant.data’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘radiant.data’ ‘radiant.basics’ ‘NeuralNetTools’ ‘car’ ‘ggplot2’
  ‘data.tree’ ‘tidyr’ ‘dplyr’ ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘radiant.data’ ‘radiant.model’ ‘dplyr’ ‘ggplot2’ ‘car’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘radiant.data’ ‘radiant.design’ ‘radiant.basics’ ‘radiant.model’
  ‘radiant.multivariate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘viridis’
Error in re-building vignettes:
  ...
radiomics: Functions for texture analysis of greyscale images.
Enter ?calc_features to see available texture features.
Quitting from lines 172-174 (TextureAnalysis.Rmd) 
Error: processing vignette ‘TextureAnalysis.Rmd’ failed with diagnostics:
there is no package called 'viridis'
Execution halted
Package required but not available: ‘rags2ridges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 20-33 (ragtop_convertibles_in_r.Rmd) 
Error: processing vignette ‘ragtop_convertibles_in_r.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘tibble’

Packages suggested but not available for checking:
  ‘dplyr’ ‘forcats’ ‘tidyr’

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

Package suggested but not available for checking: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: sp

Attaching package: 'raster'

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

    distance

Quitting from lines 36-40 (raincpc_demo.Rmd) 
Error: processing vignette ‘raincpc_demo.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘dplyr’ ‘purrr’
Error in re-building vignettes:
  ...
Quitting from lines 24-40 (intro-to-altmetric.Rmd) 
Error: processing vignette ‘intro-to-altmetric.Rmd’ failed with diagnostics:
there is no package called 'purrr'
Execution halted
Packages required but not available:
  ‘dplyr’ ‘dtplyr’ ‘DT’ ‘GGally’ ‘ggplot2’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pec’
Packages suggested but not available for checking: ‘dplyr’ ‘blockTools’
Error in re-building vignettes:
  ...
Quitting from lines 358-376 (randomizr_vignette.Rmd) 
Error: processing vignette ‘randomizr_vignette.Rmd’ failed with diagnostics:
there is no package called 'blockTools'
Execution halted
Package required but not available: ‘alphahull’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘rankhazard-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rankhazard-package
> ### Title: Rank-hazard plots
> ### Aliases: rankhazard-package rankhazard
> ### Keywords: package hplot survival
> 
> ### ** Examples
> 
> library(survival)
> model <- coxph(Surv(time,status) ~ age + sex + ph.karno, data = cancer, x=TRUE)
> rankhazardplot(model, data=cancer)
Y-axis range:  0.608 1.49 
 
Relative hazards for each covarite: 
          Min. 1st Qu. Median 3rd Qu. Max.
age      0.743   0.917      1    1.08 1.27
sex      0.608   0.608      1    1.00 1.00
ph.karno 0.766   0.875      1    1.07 1.49
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Packages required but not available: ‘hypervolume’ ‘ggplot2’

Packages suggested but not available for checking:
  ‘dplyr’ ‘gurobi’ ‘rgurobi’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pROC’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rattle’
Packages required but not available: ‘ggplot2’ ‘tidyr’ ‘dplyr’

Packages suggested but not available for checking:
  ‘arulesViz’ ‘biclust’ ‘doBy’ ‘ggdendro’ ‘ggraptR’ ‘Hmisc’ ‘mice’
  ‘odfWeave’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ChainLadder’ ‘FinCal’ ‘Lahman’ ‘nycflights13’ ‘tidyverse’
Package required but not available: ‘refGenome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rstan’ ‘bayesplot’ ‘ggplot2’ ‘dplyr’

Packages suggested but not available for checking: ‘tidyverse’ ‘rstanarm’

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

Package suggested but not available for checking: ‘spdplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’

Package suggested but not available for checking: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘gistr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘Rchoice-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estfun.Rchoice
> ### Title: Gradient for observations
> ### Aliases: estfun.Rchoice
> 
> ### ** Examples
> 
> ## Probit model
> data("Workmroz")
> probit <- Rchoice(lfp ~ k5 + k618 + age + wc + hc + lwg + inc,  
+                   data = Workmroz , family = binomial('probit'))
> summary(probit)

Model: binomial
Model estimated on: Mon Jun 25 04:35:51 PM 2018 

Call:
Rchoice(formula = lfp ~ k5 + k618 + age + wc + hc + lwg + inc, 
    data = Workmroz, family = binomial("probit"), method = "nr")


Frequencies of categories:
y
     0      1 
0.4316 0.5684 
The estimation took: 0h:0m:0s 

Coefficients:
          Estimate Std. Error z-value Pr(>|z|)    
constant  1.918422   0.380654   5.040 4.66e-07 ***
k5       -0.874711   0.113558  -7.703 1.33e-14 ***
k618     -0.038594   0.040489  -0.953 0.340488    
age      -0.037824   0.007609  -4.971 6.67e-07 ***
wc        0.488314   0.135487   3.604 0.000313 ***
hc        0.057170   0.124005   0.461 0.644776    
lwg       0.365629   0.087779   4.165 3.11e-05 ***
inc      -0.020525   0.004777  -4.297 1.73e-05 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Optimization of log-likelihood by Newton-Raphson maximisation
Log Likelihood: -452.7
Number of observations: 753
Number of iterations: 4
Exit of MLE: gradient close to zero> 
> library(sandwich)
> estfun(probit) 
Error in UseMethod("estfun") : 
  no applicable method for 'estfun' applied to an object of class "Rchoice"
Calls: estfun
Execution halted
Package required but not available: ‘hdrcde’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘mudata2’ ‘dplyr’ ‘readr’ ‘tibble’ ‘purrr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘biclust’ ‘iBBiG’ ‘superbiclust’ ‘rqubic’ ‘s4vd’ ‘BiBitR’ ‘Rcmdr’
  ‘viridis’

Depends: includes the non-default packages:
  ‘biclust’ ‘fabia’ ‘iBBiG’ ‘superbiclust’ ‘BcDiag’ ‘rqubic’ ‘BicARE’
  ‘s4vd’ ‘BiBitR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

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

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

Depends: includes the non-default packages:
  ‘Rcmdr’ ‘TeachingDemos’ ‘tseries’ ‘abind’ ‘MASS’ ‘xts’ ‘forecast’
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: ‘Rcmdr’ ‘Hmisc’

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

Packages suggested but not available for checking:
  ‘car’ ‘pROC’ ‘tableone’ ‘readxl’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘ggplot2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘ggplot2’ ‘ggthemes’

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

Package suggested but not available for checking: ‘ggplot2’

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

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

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

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

Packages suggested but not available for checking: ‘qgraph’ ‘car’ ‘Hmisc’

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

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

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

Depends: includes the non-default packages:
  ‘Rcmdr’ ‘tcltk’ ‘car’ ‘RColorBrewer’ ‘colorspace’ ‘vcd’
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: ‘Rcmdr’ ‘sutteForecastR’

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

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

Packages suggested but not available for checking: ‘Hmisc’ ‘readxl’ ‘rgl’

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

Package suggested but not available for checking: ‘FSA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘readr’ ‘DT’ ‘ggplot2’ ‘purrr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tmap’ ‘ggmap’ ‘readxl’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("RCzechia")
  Loading required package: RCzechia
  ── 1. Error: (unknown) (@test-1-data-structures.R#1)  ──────────────────────────
  there is no package called 'dplyr'
  1: library(dplyr) at testthat/test-1-data-structures.R:1
  2: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test-2-code.R#1)  ─────────────────────────────────────
  there is no package called 'dplyr'
  1: library(dplyr) at testthat/test-2-code.R:1
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test-1-data-structures.R#1) 
  2. Error: (unknown) (@test-2-code.R#1) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 27-57 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘oai’ ‘solrium’

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

Packages suggested but not available for checking: ‘rdd’ ‘rddtools’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘lpdensity’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘AER’ ‘ggplot2’ ‘rdd’

Package suggested but not available for checking: ‘car’

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

Packages suggested but not available for checking: ‘leaflet’ ‘ggplot2’

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

Packages suggested but not available for checking:
  ‘DT’ ‘tidyverse’ ‘dplyr’ ‘tidyr’ ‘tibble’ ‘purrr’ ‘repurrrsive’
  ‘nycflights13’ ‘codemetar’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘rdi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convertRDI
> ### Title: Convert RDI measures
> ### Aliases: convertRDI
> 
> ### ** Examples
> 
> 
> #create genes
> genes = sample(letters, 10000, replace=TRUE)
> #create sequence annotations
> seqAnnot = data.frame(donor = sample(1:4, 10000, replace=TRUE))
> #calculate RDI
> d = rdi(genes, seqAnnot)
> 
> ##convert RDI to actual 'lfc' estimates and compare
> dtrue = convertRDI(d)$pred
> plot(d, dtrue)
> 
> ##look at SD ranges around lfc estimates
> dtrue = convertRDI(d, calcSD=TRUE)
> 
> ##plot using ggplot2
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggthemes’ ‘tidyr’ ‘tibble’

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

Packages suggested but not available for checking: ‘qpcR’ ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘oai’ ‘solrium’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette ‘mapDWD.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Packages required but not available:
  ‘readxl’ ‘dplyr’ ‘tidyr’ ‘sjmisc’ ‘readr’

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

Package suggested but not available for checking: ‘dplyr’

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

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘streamR’ ‘readxl’ ‘readODS’

Package suggested but not available for checking: ‘quanteda’

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

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

Packages suggested but not available for checking: ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘rgl’
Error in re-building vignettes:
  ...
Loading required package: kriging
Quitting from lines 27-33 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette ‘recexcavAAR-vignette-1.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available:
  ‘dplyr’ ‘broom’ ‘tibble’ ‘purrr’ ‘tidyselect’ ‘tidyr’

Packages suggested but not available for checking: ‘rsample’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘prevR’
Packages suggested but not available for checking: ‘car’ ‘UsingR’
Packages required but not available: ‘dplyr’ ‘readr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘kableExtra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [11s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rEDM)
  > 
  > test_check("rEDM")
  ── 1. Error: make_block produces desired output (@test_02_helper_functions.R#102
  there is no package called 'tibble'
  1: tibble::as.tibble at testthat/test_02_helper_functions.R:102
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 372 SKIPPED: 0 FAILED: 1
  1. Error: make_block produces desired output (@test_02_helper_functions.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 80-84 (rEDM-coprediction.Rmd) 
Error: processing vignette ‘rEDM-coprediction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘REEMtree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: REEMtree
> ### Title: Create a RE-EM tree
> ### Aliases: REEMtree
> ### Keywords: tree models
> 
> ### ** Examples
> 
> data(simpleREEMdata)
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID)
> 
> # Estimation allowing for autocorrelation
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID, 
+ 	correlation=corAR1())
> 
> # Random parameters model for the random effects
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1+X|ID)
> 
> # Estimation with a subset
> sub <- rep(c(rep(TRUE, 10), rep(FALSE, 2)), 50)
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID, 
+ 	subset=sub)
> 
> # Dataset from the R library "AER"
> data("Grunfeld", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Package required but not available: ‘isva’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 84-116 (refinr-vignette.Rmd) 
Error: processing vignette ‘refinr-vignette.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘tibble’ ‘dplyr’

Packages suggested but not available for checking: ‘ggplot2’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘tidyr’ ‘dplyr’ ‘plotly’ ‘refund’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘caret’ ‘semPlot’
Error in re-building vignettes:
  ...
Quitting from lines 13-18 (short_intro.Rmd) 
Error: processing vignette ‘short_intro.Rmd’ failed with diagnostics:
there is no package called 'semPlot'
Execution halted
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘keras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘viridis’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 73-96 (restrictions.Rmd) 
Error: processing vignette ‘restrictions.Rmd’ failed with diagnostics:
there is no package called 'tibble'
Execution halted
Package which this enhances but not available for checking: ‘seriation’
Package required but not available: ‘PhaseType’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcmdr’
Packages required but not available: ‘plotly’ ‘data.tree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘OutbreakTools’ ‘ggplot2’ ‘geojsonio’

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

Packages suggested but not available for checking:
  ‘sparklyr’ ‘ggplot2’ ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘styler’
Packages required but not available: ‘dplyr’ ‘googledrive’ ‘quickPlot’

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

Packages suggested but not available for checking: ‘gapminder’ ‘purrr’

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

Package suggested but not available for checking: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘purrr’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testCases.R’ [1s/2s]
Running the tests in ‘tests/testCases.R’ failed.
Complete output:
  > ## test constrained lm, rlm, glm
  > # mixing weights
  > # bootstrap standard errors
  > # models with and without intercept
  > # case weights
  > # constraints on factors and interactions
  > 
  > library(restriktor)
  This is restriktor 0.1-80.711
  restriktor is BETA software! Please report any bugs.
  > n <- 100
  > p <- 4
  > betas = c(0.1,0.2,0.3,0.4,0.5)
  > set.seed(3013073)
  > X <- cbind(mvtnorm:::rmvnorm(n, mean=rep(0,p), sigma=diag(p)), rbinom(n,1,0.5))
  > colnames(X) <- c("x1","x2","x3","x4","f1")
  > z <- X %*% betas        
  > y <- z + rnorm(n)
  > DATA <- data.frame(y, X)
  > 
  > # intercept model
  > model1 <- y ~  1 + x1 + x2 + x3 + x4
  > # no intercept model
  > model2 <- y ~ -1 + x1 + x2 + x3 + x4
  > # intercept model with interaction
  > model3 <- y ~ 1 + x1*f1 + x2*f1 + x3*f1 + x4*f1
  > # intercept model with interaction
  > model4 <- y ~ -1 + x1*f1 + x2*f1 + x3*f1 + x4*f1
  > 
  > ############################ lm #################################
  > linmod1 <- lm(model1, data = DATA)
  > linmod2 <- lm(model2, data = DATA)
  > linmod3 <- lm(model3, data = DATA)
  > linmod1wt <- lm(model1, data = DATA, weights = abs(rnorm(n)))
  > linmod2wt <- lm(model2, data = DATA, weights = abs(rnorm(n)))
  > linmod1fac <- lm(model3, data = DATA)
  > linmod2fac <- lm(model4, data = DATA)
  > 
  > constraints1 <- 'x1 > 0; x2 > 0; x3 > 0'
  > fit.restr1 <- restriktor(linmod1, constraints1)
  Error in UseMethod("conLM") : 
    no applicable method for 'conLM' applied to an object of class "lm"
  Calls: restriktor
  Execution halted
Packages required but not available: ‘useful’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <single>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Loading required package: rivr
M1 profile specified. Computing upstream profile
Warning in block_exec(params) :
  failed to tidy R code in chunk <loop>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
Warning in block_exec(params) :
  failed to tidy R code in chunk <reval-single>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
Quitting from lines 73-74 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Packages suggested but not available for checking:
  ‘dplyr’ ‘ggplot2’ ‘Hmisc’
Error in re-building vignettes:
  ...
Quitting from lines 29-33 (log_parsing.Rmd) 
Error: processing vignette ‘log_parsing.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘purrr’ ‘readr’ ‘tibble’

Packages suggested but not available for checking: ‘dplyr’ ‘tidyr’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RFLPtools-package
> ### Title: Tools to analyse RFLP-data
> ### Aliases: RFLPtools-package RFLPtools
> ### Keywords: package multivariate cluster
> 
> ### ** Examples
> 
> data(RFLPdata)
> res <- RFLPdist(RFLPdata)
> plot(hclust(res[[1]]), main = "Euclidean distance")
> 
> par(mfrow = c(1,2))
> plot(hclust(RFLPdist(RFLPdata, nrBands = 3)), cex = 0.7)
> RFLPplot(RFLPdata, nrBands = 3, mar.bottom = 6, cex.axis = 0.8)
> 
> data(RFLPref)
> RFLPrefplot(RFLPdata, RFLPref, nrBands = 6, cex.axis = 0.8)
> 
> 
> library(MKmisc)
Error in library(MKmisc) : there is no package called ‘MKmisc’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: RColorBrewer

Error: processing vignette ‘RFLPtools.Rnw’ failed with diagnostics:
 chunk 5 (label = cor) 
Error in library(MKmisc) : there is no package called ‘MKmisc’
Execution halted
Packages required but not available: ‘ggplot2’ ‘UsingR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘forcats’ ‘ggplot2’ ‘purrr’ ‘tidyr’

Packages suggested but not available for checking:
  ‘DT’ ‘haven’ ‘kableExtra’ ‘readr’ ‘readxl’ ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘swfscMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘oai’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 87-88 (vignette_RGCCA.Rmd) 
Error: processing vignette ‘vignette_RGCCA.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘readr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘agricolae’ ‘Hmisc’ ‘openair’ ‘pmg’ ‘Rcmdr’ ‘rgl’ ‘RGraphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  atkClasses.c:1050:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1058:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1397:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1948:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1964:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8665:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11110:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RGtk2.Rcheck/00install.out’ for details.
Packages required but not available: ‘readr’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘GGally’ ‘ggplot2’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘readr’ ‘tibble’ ‘haven’ ‘DT’

Packages suggested but not available for checking:
  ‘plotly’ ‘ggplot2’ ‘tidyr’

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

Packages suggested but not available for checking:
  ‘feather’ ‘readODS’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘rms’

Packages suggested but not available for checking: ‘Daim’ ‘pec’ ‘pROC’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: rivr
M1 profile specified. Computing upstream profile
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Quitting from lines 96-100 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/JSONSharedString.h:297:17: warning: ‘json_shared_string::len’ will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   ‘json_shared_string::json_shared_string_internal* json_shared_string::_str’ [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: ‘JSONStream::state’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   ‘void (* JSONStream::call)(void*, void*)’ [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: ‘JSONStream::err_call’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   ‘json_string JSONStream::buffer’ [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  libjson/Source/internalJSONNode.h:257:18: warning: ‘internalJSONNode::_name_encoded’ will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   ‘json_string internalJSONNode::_name’ [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘lmerTest’
Package required but not available: ‘Luminescence’

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Luminescence’ ‘readxl’ ‘DT’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tibble’ ‘dplyr’ ‘geojsonio’ ‘tidyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘ggplot2’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘merTools’
Running examples in ‘rmcorr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.rmc
> ### Title: Plot the repeated measures correlation coefficient.
> ### Aliases: plot.rmc
> 
> ### ** Examples
> 
> ## Bland Altman 1995 data
> my.rmc <- rmcorr(participant = Subject, measure1 = PacO2, measure2 = pH, dataset = bland1995)
Warning in rmcorr(participant = Subject, measure1 = PacO2, measure2 = pH,  :
  'Subject' coerced into a factor
> plot(my.rmc, overall = TRUE)
> 
> #using ggplot instead
> ggplot2::ggplot(bland1995, ggplot2::aes(x = PacO2, y = pH, group = factor(Subject),
+       color = factor(Subject))) +
+       ggplot2::geom_point(ggplot2::aes(colour = factor(Subject))) +
+       ggplot2::geom_line(ggplot2::aes(y = my.rmc$model$fitted.values), linetype = 1) 
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Loading required package: pwr
Loading required package: psych
Loading required package: RColorBrewer
Loading required package: plotrix

Attaching package: 'plotrix'

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

    rescale

Loading required package: rmcorr
Loading required package: lme4
Loading required package: Matrix
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Loading required package: merTools
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'merTools'
Warning in rmcorr(sub, newX, newY, exampleMat) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat2) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat3) :
  'sub' coerced into a factor
Quitting from lines 470-519 (Combined_paper_figures.Rmd) 
Error: processing vignette ‘Combined_paper_figures.Rmd’ failed with diagnostics:
could not find function "predictInterval"
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggnetwork’ ‘dplyr’

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

Package suggested but not available for checking: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘Rmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: group.CI
> ### Title: Group Confidence Interval
> ### Aliases: group.CI
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> require(latticeExtra)
Loading required package: latticeExtra
Loading required package: RColorBrewer
> with(group.CI(weight~feed,chickwts),
+  segplot(feed~weight.lower+weight.upper,center=weight.mean)
+ )
> 
> require(Hmisc)
Loading required package: Hmisc
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Hmisc’
> with(group.CI(Temp~Month,airquality),
+  xYplot(Cbind(Temp.mean,Temp.lower,Temp.upper)~numericScale(Month),type="b",ylim=c(60,90))
+ )
Error in xYplot(Cbind(Temp.mean, Temp.lower, Temp.upper) ~ numericScale(Month),  : 
  could not find function "xYplot"
Calls: with -> with.default -> eval -> eval
Execution halted
Packages suggested but not available for checking: ‘readr’ ‘tidyr’ ‘dplyr’
Error in re-building vignettes:
  ...
Quitting from lines 102-131 (gff-processing.Rmd) 
Error: processing vignette ‘gff-processing.Rmd’ failed with diagnostics:
there is no package called 'readr'
Execution halted
Packages required but not available: ‘tidyverse’ ‘purrr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘ggplot2’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘pdp’ ‘purrr’ ‘tibble’ ‘viridis’

Package suggested but not available for checking: ‘openair’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘hot.deck’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
Quitting from lines 208-221 (rte-vignette_creating_exams.Rmd) 
Error: processing vignette ‘rte-vignette_creating_exams.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking:
  ‘rdflib’ ‘rfigshare’ ‘phylobase’ ‘taxize’

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

Packages suggested but not available for checking:
  ‘dendextend’ ‘DT’ ‘ggdendro’ ‘ggplot2’ ‘leaflet’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘tibble’ ‘isdparser’

Packages suggested but not available for checking:
  ‘taxize’ ‘leaflet’ ‘purrr’ ‘ggmap’ ‘ropenaq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 39-48 (RNOmni.Rmd) 
Error: processing vignette ‘RNOmni.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘rcrossref’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘car’ ‘GGally’ ‘VIM’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

 google.com                      


 google.com                      

Quitting from lines 60-62 (using_robotstxt.Rmd) 
Error: processing vignette ‘using_robotstxt.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Package required but not available: ‘GSE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘GGally’
Error in re-building vignettes:
  ...
Loading required package: robustbase
Loading required package: xtable
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘lmrob_simulation.Rnw’ failed with diagnostics:
 chunk 2 (label = graphics-setup) 
Error in eval(expr, .GlobalEnv) : require(ggplot2) is not TRUE
Execution halted
Packages required but not available: ‘ggplot2’ ‘perry’

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

Packages suggested but not available for checking: ‘tables’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘data.tree’
Error in re-building vignettes:
  ...

Attaching package: 'rODE'

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

    step

Quitting from lines 27-65 (ErrorEuler.Rmd) 
Error: processing vignette ‘ErrorEuler.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘tidyr’ ‘alphahull’
Running examples in ‘rollply-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build_grid_ahull_fill
> ### Title: Regular grid in alpha-hull
> ### Aliases: build_grid_ahull_fill
> 
> ### ** Examples
> 
> 
> data(meadow)
> 
> # Plot a grid with diagnostics
> grid <- build_grid_ahull_fill(meadow[ ,c('lon','lat')], 10000,
+                               grid_opts = list(verbose = TRUE))
Error in build_grid_ahull_fill(meadow[, c("lon", "lat")], 10000, grid_opts = list(verbose = TRUE)) : 
  Alpha-hull-based grids require package alphahull
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rollply)
  > 
  > test_check("rollply")
  ── 1. Error: inahull_cpp works (@test_inahull.R#9)  ────────────────────────────
  there is no package called 'alphahull'
  1: library(alphahull) at testthat/test_inahull.R:9
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Error: inahull_cpp works (@test_inahull.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 21-27 (rollply.Rmd) 
Error: processing vignette ‘rollply.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘openair’ ‘ggmap’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘someFIGIs.R’ [1s/5s]
Running the tests in ‘tests/someFIGIs.R’ failed.
Complete output:
  > library(ROpenFIGI)
  > jsondf <- data.frame(idType=c("ID_ISIN"),idValue=c("US922646AS37"),
  +                      exchCode=c(NA),currency=NA,micCode=NA,stringsAsFactors = F)
  > 
  > jsonrst <- OpenFIGI(jsondf)
  > jsonrst
  [[1]]
            figi                  name             ticker exchCode compositeFIGI
  1 BBG00004SPH6 REPUBLIC OF VENEZUELA VENZ 9.25 09/15/27  EUROTLX            NA
       uniqueID securityType marketSector shareClassFIGI uniqueIDFutOpt
  1 COTT3359474       GLOBAL         Govt             NA             NA
    securityType2 securityDescription
  1            NA VENZ 9 1/4 09/15/27
  
  > 
  > library(dplyr)
  Error in library(dplyr) : there is no package called 'dplyr'
  Execution halted
Packages required but not available: ‘mrfDepth’ ‘rrcovHD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘rgl’ ‘sphereplot’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘RNeXML’ ‘phylobase’ ‘fulltext’ ‘readxl’
Error in re-building vignettes:
  ...
Quitting from lines 148-152 (data_mashups.Rmd) 
Error: processing vignette ‘data_mashups.Rmd’ failed with diagnostics:
there is no package called 'phylobase'
Execution halted
Package required but not available: ‘BioGeoBEARS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘rpdo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pdo
> ### Title: Pacific Decadal Oscillation Index
> ### Aliases: pdo
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(rpdo)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: parallel
Quitting from lines 7-13 (diagnostics.Rmd) 
Error: processing vignette ‘diagnostics.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rpivotTable)
  > 
  > test_check("rpivotTable")
  ── 1. Error: (unknown) (@test_data.R#3)  ───────────────────────────────────────
  there is no package called 'dplyr'
  1: library(dplyr) at testthat/test_data.R:3
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_data.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 103-110 (rpivotTableIntroduction.Rmd) 
Error: processing vignette ‘rpivotTableIntroduction.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘solrium’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘dbplyr’
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’

Package suggested but not available for checking: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘tableone’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 16-19 (CoupledHarmonics.Rmd) 
Error: processing vignette ‘CoupledHarmonics.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘warbleR’ ‘dplyr’ ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  regTree.c:242:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RRF.Rcheck/00install.out’ for details.
Package required but not available: ‘mvoutlier’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘GGally’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘tidyr’ ‘dplyr’ ‘purrr’ ‘tibble’ ‘recipes’

Packages suggested but not available for checking: ‘ggplot2’ ‘AmesHousing’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘rgl’ ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘FactoMineR’ ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘purrr’ ‘tidyselect’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  ‘aire.zmvm’ ‘ggplot2’ ‘ggmap’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘ggplot2’

Packages suggested but not available for checking: ‘kableExtra’ ‘imager’

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

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘bayesplot’ ‘ggplot2’ ‘rstan’ ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘shinystan’ ‘bayesplot’

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

Packages suggested but not available for checking: ‘ggplot2’ ‘ggjoy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘bayesplot’ ‘rstan’ ‘rstanarm’ ‘shinystan’ ‘usethis’
Package required but not available: ‘tibble’

Package which this enhances but not available for checking: ‘ggplot2’

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

Packages suggested but not available for checking: ‘leaflet’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘rsvd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rpca
> ### Title: Randomized principal component analysis (rpca).
> ### Aliases: rpca
> 
> ### ** Examples
> 
> 
> library('rsvd')
> #
> # Load Edgar Anderson's Iris Data
> #
> data('iris')
> 
> #
> # log transform
> #
> log.iris <- log( iris[ , 1:4] )
> iris.species <- iris[ , 5]
> 
> #
> # Perform rPCA and compute only the first two PCs
> #
> iris.rpca <- rpca(log.iris, k=2)
> summary(iris.rpca) # Summary
                         PC1   PC2
Explained variance     2.933 0.907
Standard deviations    1.712 0.952
Proportion of variance 0.733 0.227
Cumulative proportion  0.733 0.960
> print(iris.rpca) # Prints the rotations
Standard deviations:
[1] 1.712 0.952

Eigenvalues:
[1] 2.933 0.907

Rotation:
                PC1    PC2
Sepal.Length -0.504 -0.455
Sepal.Width   0.302 -0.889
Petal.Length -0.577 -0.034
Petal.Width  -0.567 -0.035
> 
> #
> # Use rPCA to compute all PCs, similar to \code{prcomp}
> #
> iris.rpca <- rpca(log.iris)
> summary(iris.rpca) # Summary
                         PC1   PC2   PC3   PC4
Explained variance     2.933 0.907 0.133 0.027
Standard deviations    1.712 0.952 0.365 0.166
Proportion of variance 0.733 0.227 0.033 0.007
Cumulative proportion  0.733 0.960 0.993 1.000
> print(iris.rpca) # Prints the rotations
Standard deviations:
[1] 1.712 0.952 0.365 0.166

Eigenvalues:
[1] 2.933 0.907 0.133 0.027

Rotation:
                PC1    PC2    PC3    PC4
Sepal.Length  0.504 -0.455  0.709  0.191
Sepal.Width  -0.302 -0.889 -0.331 -0.091
Petal.Length  0.577 -0.034 -0.219 -0.786
Petal.Width   0.567 -0.035 -0.583  0.580
> plot(iris.rpca) # Produce screeplot, variable and individuls factor maps.
Error: The package 'ggplot2' is needed for this function to work. Please install it.
Execution halted
Running examples in ‘rsvg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rsvg
> ### Title: Render SVG into Bitmap
> ### Aliases: rsvg rsvg_pdf rsvg_png rsvg_ps rsvg_raw rsvg_svg rsvg_webp
> 
> ### ** Examples
> 
> # create some svg
> options(example.ask=FALSE)
> tmp <- tempfile()
> svglite::svglite(tmp, width = 10, height = 7)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = factor(cyl))
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘tidyr’ ‘purrr’
Error in re-building vignettes:
  ...
Loading required package: rtdists
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'dplyr'
Loading required package: tidyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'tidyr'
Loading required package: purrr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'purrr'
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Loading required package: binom
Quitting from lines 29-52 (reanalysis_rr98.Rmd) 
Error: processing vignette ‘reanalysis_rr98.Rmd’ failed with diagnostics:
could not find function "%>%"
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette ‘rtf.Rnw’ failed with diagnostics:
 chunk 29 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘tidyr’ ‘tibble’

Packages suggested but not available for checking: ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘rbokeh’ ‘tibble’ ‘tidyr’ ‘readr’

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

Packages suggested but not available for checking: ‘leaflet’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  bitmap.c:1594:29: warning: suggest parentheses around comparison in operand of ‘^’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rttf2pt1.Rcheck/00install.out’ for details.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘DT’ ‘ggthemes’ ‘plotly’ ‘colourpicker’ ‘tidyr’

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

Packages suggested but not available for checking: ‘ggplot2’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘readr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘keyholder’ ‘dplyr’ ‘tidyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggforce’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘bang’ ‘revdbayes’
Unavailable namespace imported from by a ':::' call: ‘revdbayes’
  See the note in ?`:::` about the use of this operator.
Packages required but not available: ‘keras’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘colourpicker’

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

Package suggested but not available for checking: ‘emmeans’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: checkFaceOrientation
> ### Title: check the orientation of a mesh
> ### Aliases: checkFaceOrientation
> 
> ### ** Examples
> 
> data(dummyhead)
> ## now we invert faces inwards
> checkFaceOrientation(dummyhead.mesh)
[1] TRUE
> dummyinward <- Morpho::invertFaces(dummyhead.mesh)
Error in loadNamespace(name) : there is no package called ‘Morpho’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘ggraph’
Running examples in ‘rvinecopulib-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.vinecop_dist
> ### Title: Plotting 'vinecop_dist' and 'vinecop' objects.
> ### Aliases: plot.vinecop_dist contour.vinecop_dist plot.vinecop
> ###   contour.vinecop plot.vinecop contour.vinecop_dist contour.vinecop
> ### Keywords: plot
> 
> ### ** Examples
> 
> # set up vine copula model
> d <- 20
> n <- 2e2
> u <- matrix(runif(n*d), n, d)
> vc <- vinecop(u, "indep")
> 
> # plot
> plot(vc, tree = c(1,2))
Error in plot.vinecop(vc, tree = c(1, 2)) : 
  The 'ggraph' package must be installed to plot.
Calls: plot -> plot.vinecop
Execution halted
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rvinecopulib)
  > 
  > test_check("rvinecopulib")
  ── 1. Error: plot functions work (@test_vinecop_dist.R#73)  ────────────────────
  The 'ggraph' package must be installed to plot.
  1: expect_silent(p <- plot(vc, edge_labels = "family", var_names = "legend")) at testthat/test_vinecop_dist.R:73
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: plot(vc, edge_labels = "family", var_names = "legend")
  10: plot.vinecop_dist(vc, edge_labels = "family", var_names = "legend")
  11: stop("The 'ggraph' package must be installed to plot.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 172 SKIPPED: 0 FAILED: 1
  1. Error: plot functions work (@test_vinecop_dist.R#73) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘tidyr’ ‘dplyr’ ‘tibble’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘viridis’ ‘ggdendro’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘tibble’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 73-75 (RxODE-covariates.Rmd) 
Error: processing vignette ‘RxODE-covariates.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘biclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tidyr’ ‘dplyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <setup>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Loading required package: grid
Warning in block_exec(params) :
  failed to tidy R code in chunk <sumchisqpow>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Loading required package: polynom
Quitting from lines 409-415 (sadists.Rnw) 
Error: processing vignette ‘sadists.Rnw’ failed with diagnostics:
could not find function "qplot"
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘saeSim’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: mvtnorm

Error: processing vignette ‘sc-intro.Rnw’ failed with diagnostics:
 chunk 1 
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Execution halted
Packages suggested but not available for checking: ‘car’ ‘ggplot2’ ‘mixer’
Errors in running code in vignettes:
when running code in ‘sandwich-OOP.Rnw’
  ...

> library("AER")

  When sourcing ‘sandwich-OOP.R’:
Error: there is no package called ‘AER’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric


Attaching package: ‘pcse’

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

    vcovPC

Loading required package: Formula
Classes and Methods for R developed in the
Political Science Computational Laboratory
Department of Political Science
Stanford University
Simon Jackman
hurdle and zeroinfl functions by Achim Zeileis
Warning in packageDescription("lme4") : no package 'lme4' was found
Error: processing vignette ‘sandwich-CL.Rnw’ failed with diagnostics:
at sandwich-CL.Rnw:1304, $ operator is invalid for atomic vectors
Execution halted
Packages required but not available: ‘tibble’ ‘dplyr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘purrr’ ‘readr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘factoextra’ ‘FactoMineR’ ‘ggplot2’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘cowplot’ ‘ggstance’ ‘ggridges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggforce’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: nlme
Quitting from lines 147-161 (Estimating-effect-sizes.Rmd) 
Error: processing vignette ‘Estimating-effect-sizes.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘readODS’ ‘haven’ ‘readxl’

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

Package suggested but not available for checking: ‘ggetho’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: ‘survey’

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

    dotchart


Error: processing vignette ‘SDaA_using_survey.Rnw’ failed with diagnostics:
 chunk 24 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘car’ ‘ggplot2’ ‘haven’ ‘DT’ ‘VIM’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘SDEFSR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotRules
> ### Title: Plot a rule set generated by a SDEFSR algorithm
> ### Aliases: plotRules
> 
> ### ** Examples
> 
> plotRules(habermanRules)
Package 'ggplot2' is not installed and must be installed to show the rule set plot. Do you want to install it? (Y/n): 
Error in plotRules(habermanRules) : Package ggplot2 is not available
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 538-540 (SDEFSRpackage.Rmd) 
Error: processing vignette ‘SDEFSRpackage.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggmap’ ‘ggsn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘sdmpredictors-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_correlation
> ### Title: Plot the correlation matrix for the provided layercodes
> ### Aliases: plot_correlation
> 
> ### ** Examples
> 
> correlation <- layers_correlation(c("BO_calcite", "BO_damin", "MS_bathy_5m"))
> p <- plot_correlation(correlation)
Error: ggplot2 needed for the 'plot_correlation' function to work. Please install it.
Execution halted
Error in re-building vignettes:
  ...
Loading required package: raster
Loading required package: sp
Loading required package: rgdal
rgdal: version: 1.3-3, (SVN revision 759)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.3.0, released 2018/05/04
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.1.0, June 1st, 2018, [PJ_VERSION: 510]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-1 
trying URL ‘http://sdmpredictors.samuelbosch.com/BO_ph_lonlat.tif’
Content type 'image/tiff' length 2518560 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL ‘http://sdmpredictors.samuelbosch.com/BO_salinity_lonlat.tif’
Content type 'image/tiff' length 5841760 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

trying URL ‘http://sdmpredictors.samuelbosch.com/BO_ph.tif’
Content type 'image/tiff' length 3201193 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

Quitting from lines 136-163 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
ggplot2 needed for the 'plot_correlation' function to work. Please install it.
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
[1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio1.bil" 
[2] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio11.bil"
[3] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio12.bil"
[4] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio14.bil"
[5] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio16.bil"
[6] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio5.bil" 
[7] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio7.bil" 

Error: processing vignette ‘sdmvspecies.Rnw’ failed with diagnostics:
 chunk 3 (label = bell_shaped_response_function) 
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘spsurvey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘styler’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘waterData’
Packages suggested but not available for checking: ‘spsurvey’ ‘readxl’
Error in re-building vignettes:
  ...
This is secr 3.1.6. For overview type ?secr
No errors found :-)
Quitting from lines 246-249 (secr-datainput.Rmd) 
Error: processing vignette ‘secr-datainput.Rmd’ failed with diagnostics:
package readxl is required for input from Excel spreadsheets
Execution halted
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘rgl’ ‘demography’ ‘tibble’ ‘labelled’ ‘forcats’
  ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘rgl’
Packages required but not available: ‘dplyr’ ‘ggplot2’

Packages suggested but not available for checking: ‘leaflet’ ‘moveHMM’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘qdap’ ‘NetworkToolbox’ ‘ggplot2’ ‘dplyr’ ‘purrr’

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

Package suggested but not available for checking: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘semTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: combinequark
> ### Title: Combine the results from the quark function
> ### Aliases: combinequark
> 
> ### ** Examples
> 
> set.seed(123321)
> dat <- HolzingerSwineford1939[,7:15]
> misspat <- matrix(runif(nrow(dat) * 9) < 0.3, nrow(dat))
> dat[misspat] <- NA
> dat <- cbind(HolzingerSwineford1939[,1:3], dat)
> 
> quark.list <- quark(data = dat, id = c(1, 2))
Data Check Passed.
ID Check Passed.
Loading required namespace: mice
Failed with error:  ‘there is no package called ‘mice’’
Error in loadNamespace(name) : there is no package called ‘mice’
Calls: quark ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggExtra’ ‘rgl’
Packages required but not available:
  ‘doBy’ ‘FactoMineR’ ‘factoextra’ ‘ggdendro’ ‘plotly’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘doBy’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘lexicon’ ‘syuzhet’ ‘textclean’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘quanteda’ ‘caret’ ‘ggthemes’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘qvalue’ ‘ggplot2’

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

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

Packages suggested but not available for checking: ‘biclust’ ‘DendSer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
trying URL ‘https://pure.strath.ac.uk/portal/files/43595106/Figure_2.zip’
downloaded 270 KB

Quitting from lines 45-52 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
there is no package called 'hyperSpec'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘cowplot’ ‘caret’ ‘dplyr’ ‘plotly’ ‘Hmisc’ ‘tidyr’
  ‘ggridges’

Packages suggested but not available for checking:
  ‘loomR’ ‘phateR’ ‘MAST’ ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘tmap’ ‘tibble’ ‘dplyr’ ‘tidyr’ ‘tidyselect’ ‘ggplot2’ ‘mapview’
Running ‘aggregate.R’ [1s/2s]
  Comparing ‘aggregate.Rout’ to ‘aggregate.Rout.save’ ...4c4
< Linking to GEOS 3.6.2, GDAL 2.3.0, proj.4 5.1.0
---
> Linking to GEOS 3.6.2, GDAL 2.2.3, proj.4 4.9.3
  Running ‘cast.R’ [1s/1s]
  Comparing ‘cast.Rout’ to ‘cast.Rout.save’ ... OK
  Running ‘crs.R’ [1s/1s]
  Comparing ‘crs.Rout’ to ‘crs.Rout.save’ ...75,76c75,76
< [1,]      0.0      0.0
< [2,] 111319.5 111325.1
---
> [1,]      0.0 -7.081155e-10
> [2,] 111319.5  1.113251e+05
85c85
< bbox:           xmin: 0 ymin: 0 xmax: 111319.5 ymax: 111325.1
---
> bbox:           xmin: 0 ymin: -7.081155e-10 xmax: 111319.5 ymax: 111325.1
88c88
< POINT (0 0)
---
> POINT (0 -7.081155e-10)
  Running ‘dist.R’ [2s/2s]
  Comparing ‘dist.Rout’ to ‘dist.Rout.save’ ...97c97
< bbox:           xmin: 0 ymin: 0 xmax: 10625.95 ymax: 110823.7
---
> bbox:           xmin: 0 ymin: -7.081155e-10 xmax: 10625.95 ymax: 110823.7
101c101
< MULTIPOINT (505.9977 0, 1517.993 0, 2529.988 0,...
---
> MULTIPOINT (505.9977 -7.081155e-10, 1517.993 -7...
  Running ‘dplyr.R’ [1s/1s]
Running the tests in ‘tests/dplyr.R’ failed.
Complete output:
  > suppressPackageStartupMessages(library(sf))
  > library(dplyr)
  Error in library(dplyr) : there is no package called 'dplyr'
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 461-462 (sf1.Rmd) 
Error: processing vignette ‘sf1.Rmd’ failed with diagnostics:
package tibble not available: install first?
Execution halted
Package required but not available: ‘tensorflow’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SGP’
Error in re-building vignettes:
  ...
Quitting from lines 2-11 (SGPdata.Rmd) 
Error: processing vignette ‘SGPdata.Rmd’ failed with diagnostics:
there is no package called 'toOrdinal'
Execution halted
Package suggested but not available for checking: ‘threejs’
Packages required but not available: ‘aqp’ ‘soilDB’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘alakazam’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tidyr’ ‘ggExtra’

Package suggested but not available for checking: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘shinyaframe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aDataScene
> ### Title: A-Frame Scene with R data
> ### Aliases: aDataScene
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Package suggested but not available for checking: ‘colourpicker’
Packages required but not available:
  ‘heatmaply’ ‘dplyr’ ‘viridis’ ‘plotly’ ‘readxl’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DT’ ‘difNLR’ ‘ggplot2’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘highcharter’
Running examples in ‘shinyjqui-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Interactions
> ### Title: Mouse interactions
> ### Aliases: Interactions jqui_resizabled jqui_sortabled jqui_draggabled
> ###   jqui_droppabled jqui_selectabled jqui_sortable jqui_draggable
> ###   jqui_droppable jqui_selectable jqui_resizable
> 
> ### ** Examples
> 
> library(shiny)
> library(highcharter)
Error in library(highcharter) : there is no package called ‘highcharter’
Execution halted
Package required but not available: ‘purrr’

Packages suggested but not available for checking: ‘dplyr’ ‘gapminder’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘bayesplot’ ‘colourpicker’ ‘DT’ ‘ggplot2’ ‘rstan’ ‘threejs’

Package suggested but not available for checking: ‘rstanarm’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tidyr’

Package suggested but not available for checking: ‘MplusAutomation’

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

Depends: includes the non-default packages:
  ‘hdrcde’ ‘coda’ ‘MASS’ ‘bayesm’ ‘mnormt’ ‘spatstat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘hdrcde’ ‘viridis’ ‘tidyr’ ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’

Packages suggested but not available for checking: ‘cowplot’ ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 59-67 (sigmoid.Rmd) 
Error: processing vignette ‘sigmoid.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘phylobase’ ‘phyext2’ ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘SimMultiCorrData’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘robCompositions’
Error in re-building vignettes:
  ...
Loading required package: Rcpp
Loading required package: lattice
Loading required package: parallel
Loading required package: boot

Attaching package: ‘boot’

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

    melanoma

Loading required package: MASS

Error: processing vignette ‘simFrame-intro.Rnw’ failed with diagnostics:
 chunk 23 
Error in library("robCompositions") : 
  there is no package called ‘robCompositions’
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘broom’

Packages suggested but not available for checking: ‘ggplot2’ ‘tidyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘DiagrammeR’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘simmer.plot’ ‘dplyr’ ‘tidyr’
Packages required but not available: ‘VIM’ ‘EnvStats’

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: ‘dplyr’ ‘VIM’
Packages required but not available:
  ‘SimMultiCorrData’ ‘SimCorrMix’ ‘ggplot2’

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

Package suggested but not available for checking: ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘simstudy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addCondition
> ### Title: Add a single column to existing data set based on a condition
> ### Aliases: addCondition
> 
> ### ** Examples
> 
> 
> # New data set
> 
> def <- defData(varname = "x", dist = "categorical", formula = ".33;.33")
> def <- defData(def, varname="y", dist="uniform", formula="-5;5")
> 
> dt <- genData(1000, def)
> 
> # Define conditions
> 
> defC <- defCondition(condition = "x == 1", formula = "5 + 2*y-.5*y^2",
+                      variance = 1,dist = "normal")
> defC <- defCondition(defC, condition = "x == 2",
+                      formula = "3 - 3*y + y^2", variance = 2, dist="normal")
> defC <- defCondition(defC, condition = "x == 3",
+                      formula = "abs(y)", dist="poisson")
> 
> # Add column
> 
> dt <- addCondition(defC, dt, "NewVar")
> 
> # Plot data
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: data.table
Quitting from lines 38-282 (simstudy.Rmd) 
Error: processing vignette ‘simstudy.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’ ‘tibble’

Packages suggested but not available for checking: ‘ggplot2’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [34s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Got this Sys.setenv line from https://github.com/luckyrandom/cmaker/blob/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0/tests/testthat.R
  > # so that devtools:check() won't hang.
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(simulator)
  
  Attaching package: 'simulator'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("simulator")
  ── 1. Failure: create makes a template that can be run without error (@test-crea
  any(grepl("error", readLines(a), ignore.case = TRUE)) isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 119 SKIPPED: 3 FAILED: 1
  1. Failure: create makes a template that can be run without error (@test-create.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘miceadds’
Packages required but not available: ‘tibble’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 130-154 (uniform_rng_with_sitmo.Rmd) 
Error: processing vignette ‘uniform_rng_with_sitmo.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘SiZer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Arkansas
> ### Title: Time Series of Macroinvertabrates Abundance in the Arkansas
> ###   River.
> ### Aliases: Arkansas
> ### Keywords: datasets
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> 
> data(Arkansas)
> ggplot(Arkansas, aes(x=year, y=sqrt.mayflies)) + 
+    geom_point()
Error in ggplot(Arkansas, aes(x = year, y = sqrt.mayflies)) : 
  could not find function "ggplot"
Execution halted
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘haven’ ‘purrr’ ‘tibble’ ‘tidyselect’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘Hmisc’ ‘sjmisc’ ‘sjPlot’ ‘Zelig’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘haven’ ‘purrr’ ‘sjlabelled’ ‘tibble’ ‘tidyr’
  ‘tidyselect’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘mice’ ‘sjPlot’ ‘sjstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘forcats’ ‘ggeffects’ ‘ggplot2’ ‘merTools’ ‘modelr’
  ‘purrr’ ‘sjlabelled’ ‘sjmisc’ ‘sjstats’ ‘tidyselect’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘car’ ‘ggrepel’ ‘ggridges’ ‘lmerTest’ ‘rstanarm’ ‘viridis’ ‘Zelig’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘bayesplot’ ‘broom’ ‘dplyr’ ‘emmeans’ ‘modelr’ ‘purrr’ ‘sjlabelled’
  ‘sjmisc’ ‘tidyr’ ‘tidyselect’ ‘tibble’

Packages suggested but not available for checking:
  ‘AER’ ‘apaTables’ ‘brms’ ‘car’ ‘ggplot2’ ‘ggridges’ ‘mediation’
  ‘pROC’ ‘sjPlot’ ‘rstan’ ‘rstanarm’ ‘Zelig’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘adegenet’ ‘hierfstat’ ‘pegas’ ‘rmetasim’ ‘strataG’ ‘swfscMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’ ‘tidyselect’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘ggrepel’

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘agricolae’ ‘car’ ‘mosaic’
Error in re-building vignettes:
  ...
Loading required package: mosaic
Loading required package: Sleuth2
Quitting from lines 130-145 (chapter01-HortonMosaic.Rnw) 
Error: processing vignette ‘chapter01-HortonMosaic.Rnw’ failed with diagnostics:
could not find function "trellis.par.set"
Execution halted
Packages suggested but not available for checking:
  ‘Hmisc’ ‘agricolae’ ‘car’ ‘mosaic’
Error in re-building vignettes:
  ...
Loading required package: mosaic
Loading required package: Sleuth3
Quitting from lines 130-145 (chapter01-HortonMosaic.Rnw) 
Error: processing vignette ‘chapter01-HortonMosaic.Rnw’ failed with diagnostics:
could not find function "trellis.par.set"
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 65-69 (slim.Rmd) 
Error: processing vignette ‘slim.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘Hmisc’ ‘weights’ ‘candisc’

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

Package suggested but not available for checking: ‘demography’

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

Package suggested but not available for checking: ‘Mcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘imager’ ‘ggplot2’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘sm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sm.surface3d
> ### Title: Adding a regression surface to an rgl plot.
> ### Aliases: sm.surface3d
> ### Keywords: nonparametric regression smooth
> 
> ### ** Examples
> 
> with(trawl, {
+    Zone93    <- (Year == 1 & Zone == 1)
+    Position  <- cbind(Longitude - 143, Latitude)
+    model1 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.1, 0.1), display = "rgl", xlab="Longitude - 143")
+    model2 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.2, 0.2), display = "none")
+    sm.surface3d(model2$eval.points, model2$est, model1$scaling, col = "red")
+ })
Error in sm.surface3d(model2$eval.points, model2$est, model1$scaling,  : 
  a scaling must be specified.
Calls: with -> with.default -> eval -> eval -> sm.surface3d
Execution halted
Packages suggested but not available for checking: ‘tibble’ ‘purrrlyr’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("tibble")
  Error in library("tibble") : there is no package called 'tibble'
  Execution halted
Packages required but not available: ‘car’ ‘ggplot2’ ‘rgl’

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

Package suggested but not available for checking: ‘ggplot2’

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

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

Package suggested but not available for checking: ‘plotKML’

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

Package suggested but not available for checking: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Sotkanet R tools (C) 2013-2017 rOpenGov
https://github.com/ropengov/sotkanet
Retrieving indicator 10013
Quitting from lines 99-114 (tutorial.Rmd) 
Error: processing vignette ‘tutorial.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘r2cytoscape’
Running examples in ‘SourceSet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: easyLookSource
> ### Title: Easy look results
> ### Aliases: easyLookSource
> 
> ### ** Examples
> 
> ## Load the SourceSetObj obtained from the source set analysis of ALL dataset
> 
> # see vignette for more details
> print(load(file=system.file("extdata","ALLsourceresult.RData",package = "SourceSet")))
[1] "results.all"
> class(results.all)
[1] "sourceSetList"
> n.primary<-length(lapply(results.all,function(x) x$primarySet))
> 
> # show only genes that appear in at least one of the source sets of the investigated pathways
> easyLookSource(sourceObj=results.all, maxnum.variable = n.primary,
+                label.variable = "Genes",label.graph = "Pathways")
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: easyLookSource ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 1.38 secs
Quitting from lines 311-312 (SourceSet.Rmd) 
Error: processing vignette ‘SourceSet.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘quickPlot’ ‘reproducible’ ‘DiagrammeR’ ‘dplyr’

Package suggested but not available for checking: ‘SpaDES.tools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘quickPlot’ ‘reproducible’ ‘SpaDES.addins’ ‘SpaDES.core’
  ‘SpaDES.tools’

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

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘earlywarnings’
Package suggested but not available for checking: ‘Infusion’
Packages required but not available: ‘sparklyr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘dbplyr’ ‘readr’ ‘tidyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘Lahman’ ‘nycflights13’ ‘tibble’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘RGraphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 1270-1273 (sparseHessianFD.Rnw) 
Error: processing vignette ‘sparseHessianFD.Rnw’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 73-87 (sparseMVN.Rnw) 
Error: processing vignette ‘sparseMVN.Rnw’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘readr’ ‘rms’ ‘EnvStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘leaflet’

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plot3Drgl’

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

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

Packages suggested but not available for checking:
  ‘ggplot2’ ‘broom’ ‘ggpolypath’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘spbabel’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘imager’ ‘tidyverse’ ‘rgl’
Packages required but not available:
  ‘hyperSpec’ ‘rgl’ ‘GGally’ ‘ggplot2’ ‘ggdendro’ ‘caret’ ‘qdap’ ‘xcms’
  ‘MAIT’ ‘speaq’

Package suggested but not available for checking: ‘rcytoscapejs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘NMF’ ‘plotly’ ‘viridis’ ‘hNMF’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggmap’ ‘ggplot2’
Running examples in ‘spew-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_pop_totals
> ### Title: Plot characteristic summary output from
> ###   summarize_top_spew_region as totals
> ### Aliases: plot_pop_totals
> 
> ### ** Examples
> 
> data(tartanville)
> 
> tartanville_syneco <- spew(tartanville$pop_table, tartanville$shapefile, 
+                            tartanville$pums_h, tartanville$pums_p)
Loading required package: sp
[1] "Place has 0 Households!"
> plot_syneco(tartanville, tartanville_syneco, region_name = "Tartanville")
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: plot_syneco ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running ‘testthat.R’ [23s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spew)
  > 
  > test_check("spew")
  ── 1. Error: functions for summarizing spew synecos in console (@test-summarize-
  there is no package called 'ggplot2'
  1: ggplot2::fortify at testthat/test-summarize-spew.R:6
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 100 SKIPPED: 7 FAILED: 1
  1. Error: functions for summarizing spew synecos in console (@test-summarize-spew.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Quitting from lines 45-64 (spew-quickstart.Rmd) 
Error: processing vignette ‘spew-quickstart.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘quadmesh’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mlr’ ‘ggplot2’

Package suggested but not available for checking: ‘caret’

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

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

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘antaresViz’
Package required but not available: ‘biomod2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘rgbif’ ‘rbison’ ‘rebird’ ‘rvertnet’ ‘tibble’

Package suggested but not available for checking: ‘taxize’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  wdl.cpp:184:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spp.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  points.within
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'points.within':
  ‘points.within’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘swfscMisc’

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

Packages suggested but not available for checking: ‘dplyr’ ‘GGally’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘autothresholdr’ ‘viridis’ ‘ggplot2’ ‘imager’

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

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

Packages suggested but not available for checking: ‘dbplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ssc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coBC
> ### Title: CoBC method
> ### Aliases: coBC
> 
> ### ** Examples
> 
> 
> library(ssc)
> 
> ## Load Wine data set
> data(wine)
> 
> cls <- which(colnames(wine) == "Wine")
> x <- wine[, -cls] # instances without classes
> y <- wine[, cls] # the classes
> x <- scale(x) # scale the attributes
> 
> ## Prepare data
> set.seed(20)
> # Use 50% of instances for training
> tra.idx <- sample(x = length(y), size = ceiling(length(y) * 0.5))
> xtrain <- x[tra.idx,] # training instances
> ytrain <- y[tra.idx]  # classes of training instances
> # Use 70% of train instances as unlabeled set
> tra.na.idx <- sample(x = length(tra.idx), size = ceiling(length(tra.idx) * 0.7))
> ytrain[tra.na.idx] <- NA # remove class information of unlabeled instances
> 
> # Use the other 50% of instances for inductive testing
> tst.idx <- setdiff(1:length(y), tra.idx)
> xitest <- x[tst.idx,] # testing instances
> yitest <- y[tst.idx] # classes of testing instances
> 
> ## Example: Training from a set of instances with 1-NN as base classifier.
> set.seed(1)
> m1 <- coBC(x = xtrain, y = ytrain, 
+            learner = caret::knn3, 
+            learner.pars = list(k = 1),
+            pred = "predict")
Error in loadNamespace(name) : there is no package called ‘caret’
Calls: coBC ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘caret’ ‘klaR’

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.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘ggfortify’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘Hmisc’ ‘dplyr’

Package suggested but not available for checking: ‘viridis’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘afex’ ‘lmerTest’
Error in re-building vignettes:
  ...
Quitting from lines 362-367 (using-standardize.Rmd) 
Error: processing vignette ‘using-standardize.Rmd’ failed with diagnostics:
there is no package called 'afex'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 47-52 (staple_example.Rmd) 
Error: processing vignette ‘staple_example.Rmd’ failed with diagnostics:
incorrect number of dimensions
Execution halted
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘eemR’ ‘readr’ ‘tibble’ ‘plotly’ ‘GGally’
  ‘drc’

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  ‘AER’ ‘dynlm’ ‘erer’ ‘rms’ ‘sampleSelection’ ‘Zelig’
Packages required but not available:
  ‘readr’ ‘tidyr’ ‘purrr’ ‘ggplot2’ ‘ggdendro’ ‘ggrepel’

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

Packages suggested but not available for checking: ‘tidyverse’ ‘leaflet’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: proxy

Attaching package: ‘proxy’

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

    as.dist, dist

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

    as.matrix

Loading required package: clue
Loading required package: survey
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: ‘survey’

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

    dotchart

Loading required package: RANN
Loading required package: lpSolve
Loading required package: Hmisc

Error: processing vignette ‘Statistical_Matching_with_StatMatch.Rnw’ failed with diagnostics:
 chunk 4 
Error in spearman2(n.income ~ area5 + urb + hsize + age + sex + marital +  : 
  could not find function "spearman2"
Execution halted
Package suggested but not available for checking: ‘EpiModel’
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘statnet’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘statnet’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/statnet.Rcheck/00install.out’ for details.
Package required but not available: ‘tidytext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tibble’ ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘broom’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [6s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stellaRbase)
  > 
  > options(scipen = 25)
  > 
  > test_check("stellaRbase")
  ── 1. Failure: Row counts are correct. (@test-getEffects_Account.R#33)  ────────
  t2[["_embedded"]][["records"]] has length 3, not length 2.
  
  ── 2. Failure: Row counts are correct and consolidate between lists and data tab
  nrow(t8) not equal to 2.
  1/1 mismatches
  [1] 3 - 2 == 1
  
  ── 3. Failure: Row counts are as expected. (@test-getPayments_Account.R#30)  ───
  t2[["_embedded"]][["records"]] has length 2, not length 1.
  
  ── 4. Failure: Row counts consolidate between lists and data tables. (@test-getP
  nrow(t6) not equal to 1.
  1/1 mismatches
  [1] 2 - 1 == 1
  
  ── 5. Failure: Row counts are as expected. (@test-getTransactions_Account.R#31) 
  t2[["_embedded"]][["records"]] has length 2, not length 1.
  
  ── 6. Failure: Row counts consolidate between lists and data tables. (@test-getT
  nrow(t7) not equal to 1.
  1/1 mismatches
  [1] 2 - 1 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 208 SKIPPED: 0 FAILED: 6
  1. Failure: Row counts are correct. (@test-getEffects_Account.R#33) 
  2. Failure: Row counts are correct and consolidate between lists and data tables. (@test-getEffects_Account.R#52) 
  3. Failure: Row counts are as expected. (@test-getPayments_Account.R#30) 
  4. Failure: Row counts consolidate between lists and data tables. (@test-getPayments_Account.R#39) 
  5. Failure: Row counts are as expected. (@test-getTransactions_Account.R#31) 
  6. Failure: Row counts consolidate between lists and data tables. (@test-getTransactions_Account.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘stm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘stm’ ‘tidygraph’ ‘ggraph’ ‘ggrepel’ ‘ggplot2’ ‘purrr’ ‘dplyr’
  ‘tibble’

Package suggested but not available for checking: ‘quanteda’

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

Package suggested but not available for checking: ‘demography’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’

Packages suggested but not available for checking:
  ‘ggmap’ ‘tigris’ ‘viridis’

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

Package suggested but not available for checking: ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’

Packages suggested but not available for checking: ‘dtplyr’ ‘mvoutlier’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘apex’ ‘adegenet’ ‘DT’ ‘ggplot2’ ‘Hmisc’ ‘pegas’ ‘swfscMisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Building shared library for Rcpp code chunk...
Quitting from lines 60-85 (strider.Rmd) 
Error: processing vignette ‘strider.Rmd’ failed with diagnostics:
Package 'BH' referenced from Rcpp::depends in source file filef1b4029030a.cpp is not available.
Execution halted
Packages required but not available:
  ‘broom’ ‘car’ ‘ggplot2’ ‘lmerTest’ ‘phia’

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

Package suggested but not available for checking: ‘demography’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘car’ ‘dynlm’
Error in re-building vignettes:
  ...
Loading required package: StructFDR
Loading required package: nlme
Loading required package: ape
Loading required package: cluster
Loading required package: dirmult
Loading required package: matrixStats
Loading required package: ggplot2
Loading required package: reshape
Quitting from lines 172-187 (StructFDR.Rmd) 
Error: processing vignette ‘StructFDR.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘rematch2’ ‘tibble’

Packages suggested but not available for checking: ‘data.tree’ ‘dplyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘purrr’ ‘readr’ ‘tidyr’ ‘tsibble’

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘d3r’ ‘dplyr’

Package suggested but not available for checking: ‘tidyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘ggdendro’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘bartMachine’ ‘caret’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 191-213 (Guide-to-SuperLearner.Rmd) 
Error: processing vignette ‘Guide-to-SuperLearner.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggformula’ ‘mosaic’
Package required but not available: ‘prim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rms’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘survAUC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: schemper
> ### Title: Distance-based estimator of survival predictive accuracy
> ###   proposed by Schemper and Henderson
> ### Aliases: schemper
> ### Keywords: classif
> 
> ### ** Examples
> 
> 
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Packages suggested but not available for checking:
  ‘rmapshaper’ ‘INLA’ ‘ggplot2’
Packages required but not available: ‘rms’ ‘rstan’

Packages suggested but not available for checking: ‘shinystan’ ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘cowplot’ ‘ggthemes’ ‘viridis’

Packages suggested but not available for checking: ‘broom’ ‘readr’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggpubr’ ‘broom’ ‘dplyr’ ‘tidyr’ ‘survMisc’ ‘purrr’
  ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘ggsci’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘broom’

Package suggested but not available for checking: ‘tidyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tsDyn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘forecast’ ‘tibble’ ‘tidyr’ ‘timetk’

Packages suggested but not available for checking:
  ‘forcats’ ‘purrr’ ‘readr’ ‘robets’ ‘tidyquant’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘SWMPr’ ‘broom’ ‘dplyr’ ‘EnvStats’ ‘ggplot2’ ‘ggthemes’ ‘leaflet’
  ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggmap’ ‘dplyr’ ‘openair’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘clusterSim’ ‘rgl’ ‘shapes’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert.mpoly
> ### Title: Convert between mpoly and list representations of multivariate
> ###   polynomials
> ### Aliases: ' convert.mpoly '
> 
> ### ** Examples
> 
> # create an mpoly object here
> 
> # convert from mpoly to list representation
> library(mpoly)
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: cubature
Loading required package: combinat

Attaching package: ‘combinat’

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

    combn

Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

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

    deriv

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

    single


Error: processing vignette ‘symmoments.rnw’ failed with diagnostics:
 chunk 13 (label = noncentral3a) 
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘readxl’

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

Package suggested but not available for checking: ‘ggplot2’

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

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘tabplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: num2fac
> ### Title: Transform a numerical vector to a factor
> ### Aliases: num2fac
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> data(diamonds)
Warning in data(diamonds) : data set ‘diamonds’ not found
> 
> diamonds$price2 <- num2fac(diamonds$price)
Loading required namespace: classInt
Error in quantile(num, na.rm = TRUE) : object 'diamonds' not found
Calls: num2fac -> quantile
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 19-24 (tabplot-timings.Rmd) 
Error: processing vignette ‘tabplot-timings.Rmd’ failed with diagnostics:
object ‘diamonds’ not found
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘spex’ ‘spbabel’ ‘tibble’ ‘viridis’ ‘gibble’

Package suggested but not available for checking: ‘spdplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 100-103 (new-methods.Rmd) 
Error: processing vignette ‘new-methods.Rmd’ failed with diagnostics:
there is no package called 'forecast'
Execution halted
Packages required but not available:
  ‘broom’ ‘pixiedust’ ‘car’ ‘ggplot2’ ‘viridis’

Package suggested but not available for checking: ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pmatch’
Packages suggested but not available for checking: ‘LSAmitR’ ‘miceadds’
Packages suggested but not available for checking: ‘rms’ ‘Hmisc’
Error in re-building vignettes:
  ...
Quitting from lines 13-18 (fda-example.Rmd) 
Error: processing vignette ‘fda-example.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘kableExtra’

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

Packages suggested but not available for checking: ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘tidyr’ ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘bold’ ‘ritis’ ‘tibble’ ‘worrms’ ‘natserv’ ‘wikitaxa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘cowplot’

Packages suggested but not available for checking: ‘tcgsaseq’ ‘GEOquery’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘DESeq2’

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

Package suggested but not available for checking: ‘dplyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘DT’ ‘leaflet’ ‘threejs’ ‘d3heatmap’ ‘tidyr’ ‘plotly’
  ‘DiagrammeR’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rgl’ ‘ggplot2’ ‘R2wd’
Packages suggested but not available for checking:
  ‘Lahman’ ‘dplyr’ ‘ggplot2’
Package required but not available: ‘eva’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘arulesViz’ ‘ggplot2’

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

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

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

Packages suggested but not available for checking: ‘keras’ ‘tfestimators’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘tergm’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘tergm’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tergm.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 29-51 (GIAValidationExample.Rmd) 
Error: processing vignette ‘GIAValidationExample.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘tidyr’ ‘FactoMineR’ ‘tibble’ ‘ggrepel’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘GGally’

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

Packages which this enhances but not available for checking:
  ‘AER’ ‘dynlm’ ‘erer’ ‘rms’ ‘sampleSelection’ ‘systemfit’ ‘xergm’
Package required but not available: ‘lexicon’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: textrank_candidates_lsh
> ### Title: Use locality-sensitive hashing to get combinations of sentences
> ###   which contain words which are in the same minhash bucket
> ### Aliases: textrank_candidates_lsh
> 
> ### ** Examples
> 
> library(textreuse)
Error in library(textreuse) : there is no package called ‘textreuse’
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 140-149 (textrank.Rmd) 
Error: processing vignette ‘textrank.Rmd’ failed with diagnostics:
there is no package called 'textreuse'
Execution halted
Packages required but not available:
  ‘dplyr’ ‘lexicon’ ‘quanteda’ ‘textclean’

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

Packages suggested but not available for checking: ‘tfestimators’ ‘keras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tensorflow’ ‘tfruns’ ‘tidyselect’ ‘purrr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking: ‘ggplot2’ ‘modelr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘plotly’ ‘rstan’ ‘stm’

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘phyloseq’ ‘tidyverse’ ‘tidyr’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forecast’ ‘hts’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘nycflights13’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tibble.Rcheck/00install.out’ for details.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’

Packages suggested but not available for checking:
  ‘broom’ ‘gapminder’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘modelr’ ‘purrr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tigris’ ‘purrr’ ‘tidyr’ ‘readr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’ ‘fuzzyjoin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking: ‘data.tree’ ‘seriation’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘forcats’ ‘ggplot2’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘broom’ ‘rsample’ ‘tidyr’ ‘dplyr’ ‘rstanarm’ ‘purrr’
  ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking: ‘dbplyr’ ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyverse’ ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tibble’ ‘tidyr’ ‘timetk’

Packages suggested but not available for checking:
  ‘alphavantager’ ‘broom’ ‘tibbletime’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyselect’

Package suggested but not available for checking: ‘gapminder’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tibble’ ‘readr’ ‘tidyr’ ‘dplyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘broom’ ‘purrr’

Packages suggested but not available for checking:
  ‘readr’ ‘tidyr’ ‘quanteda’ ‘ggplot2’ ‘gutenbergr’ ‘stm’

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

Packages suggested but not available for checking: ‘ggtree’ ‘treeio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘dbplyr’ ‘forcats’ ‘ggplot2’ ‘haven’ ‘modelr’ ‘purrr’
  ‘readr’ ‘readxl’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘feather’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘readxl’ ‘dplyr’ ‘tidyr’ ‘purrr’ ‘tibble’ ‘ggplot2’ ‘cellranger’
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyxl)
  > 
  > test_check("tidyxl")
  ── 1. Error: (unknown) (@test-names.R#3)  ──────────────────────────────────────
  there is no package called 'tibble'
  1: library(tibble) at testthat/test-names.R:3
  2: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test-validation.R#3)  ─────────────────────────────────
  there is no package called 'tibble'
  1: library(tibble) at testthat/test-validation.R:3
  2: stop(txt, domain = NA)
  
  ── 3. Error: (unknown) (@test-xlex.R#3)  ───────────────────────────────────────
  there is no package called 'tibble'
  1: library(tibble) at testthat/test-xlex.R:3
  2: stop(txt, domain = NA)
  
  ── 4. Error: (unknown) (@test-xlsx_color_theme.R#3)  ───────────────────────────
  there is no package called 'tibble'
  1: library(tibble) at testthat/test-xlsx_color_theme.R:3
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 258 SKIPPED: 0 FAILED: 4
  1. Error: (unknown) (@test-names.R#3) 
  2. Error: (unknown) (@test-validation.R#3) 
  3. Error: (unknown) (@test-xlex.R#3) 
  4. Error: (unknown) (@test-xlsx_color_theme.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 34-39 (data-validation-rules.Rmd) 
Error: processing vignette ‘data-validation-rules.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘abd’ ‘mosaic’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘alakazam’ ‘tidyr’ ‘dplyr’

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

Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggthemes’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘leaflet’
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘mtconnectR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘TimeProjection-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCalendarHeatmap
> ### Title: Calendar Heatmap
> ### Aliases: plotCalendarHeatmap
> 
> ### ** Examples
> 
> dates = timeSequence(from = '2012-01-01', to = '2012-12-31', by = 'day')
>    plotCalendarHeatmap(as.Date(dates), 1:366)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
Loading required package: plyr

Attaching package: ‘plyr’

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

    here

Error in ggplot(tp, aes(monthweek, weekday, fill = values)) : 
  could not find function "ggplot"
Calls: plotCalendarHeatmap
Execution halted
Packages required but not available:
  ‘dplyr’ ‘forecast’ ‘padr’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘broom’ ‘forcats’ ‘robets’ ‘tidyverse’ ‘tidyquant’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 18-23 (tintHTML.Rmd) 
Error: processing vignette ‘tintHTML.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘broom’ ‘tibble’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘ggplot2’
Package required but not available: ‘Luminescence’

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

Packages suggested but not available for checking:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’

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

Packages suggested but not available for checking: ‘tmap’ ‘OpenStreetMap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pca3d’
Error in re-building vignettes:
  ...
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'pca3d'
Quitting from lines 694-697 (tmod.rmd) 
Error: processing vignette ‘tmod.rmd’ failed with diagnostics:
unused argument (group = c("CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB"))
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggthemes’ ‘ggmap’ ‘GGally’

Package suggested but not available for checking: ‘ggnetwork’

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

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

Packages suggested but not available for checking: ‘ggmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rmongodb’ ‘ggplot2’
Error in re-building vignettes:
  ...
Loading required package: data.table
tcpl (v1.4.3) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in tcpl config file. See ?tcplConf for more information.
toxboot 0.1.1
MongoDB settings (?toxbootConf):
  TOXBOOT_HOST: NA
  TOXBOOT_DBNS: NA
  TOXBOOT_USER: NA
  TOXBOOT_DB: NA
MySQL settings:
  Host: Not Configured
  Database: Not Configured
  User: Not Configured
Loading required package: DBI
Quitting from lines 27-35 (toxboot.Rmd) 
Error: processing vignette ‘toxboot.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘ggthemes’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘lgtdl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ci.plot: no visible global function definition for ‘gaussian’
ci.plot: no visible global function definition for ‘qnorm’
ci.plot: no visible global function definition for ‘plot’
ci.plot: no visible global function definition for ‘lines’
cst.fit.ff: no visible global function definition for ‘pnorm’
cstfit.1: no visible global function definition for ‘var’
gof.test.boots.pf: no visible binding for global variable ‘sd’
gof.test.int.1.ff: no visible global function definition for ‘quantile’
gof.test.int.1.ff: no visible global function definition for ‘var’
gof.test.int.ff: no visible global function definition for ‘pnorm’
gofTest: no visible binding for global variable ‘sd’
plotGof: no visible global function definition for ‘plot’
plotGof : <anonymous>: no visible global function definition for
  ‘lines’
plotGof: no visible global function definition for ‘lines’
sig.test.int.1.ff: no visible global function definition for ‘quantile’
sig.test.int.1.ff: no visible global function definition for ‘var’
sig.test.int.ff: no visible global function definition for ‘pnorm’
test.boots.1: no visible binding for global variable ‘sd’
tpr: no visible global function definition for ‘poisson’
tpr: no visible global function definition for ‘glm.fit’
tpr: no visible global function definition for ‘coef’
tpr: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx coef gaussian glm.fit lines plot pnorm poisson qnorm quantile
  sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "coef", "gaussian", "glm.fit", "pnorm",
             "poisson", "qnorm", "quantile", "sd", "var")
to your NAMESPACE file.
Rd file 'ci.plot.Rd':
  \usage lines wider than 90 characters:
     ci.plot(x, y, se, level = 0.95, ylim = NULL, newplot = TRUE, fun = gaussian()$linkinv, dfun = gaussian()$mu.eta, ...)

These lines will be truncated in the PDF manual.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: ‘readxl’ ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggmap’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘dplyr’ ‘RSelenium’

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

Package suggested but not available for checking: ‘ggplot2’

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

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘TrajDataMining-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: owMeratniaByCollection
> ### Title: Ow Meratnial By Collection
> ### Aliases: owMeratniaByCollection
> ###   owMeratniaByCollection,TracksCollection,numeric,numeric-method
> 
> ### ** Examples
> 
> 
> library(magrittr)
> 
> library(sp)
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 36-42 (TrajDataMining.Rmd) 
Error: processing vignette ‘TrajDataMining.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘rgl’ ‘OpenStreetMap’
Error in re-building vignettes:
  ...

Error: processing vignette ‘tracks.Rnw’ failed with diagnostics:
 chunk 1 
Error in library("rgl") : there is no package called ‘rgl’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: trapezoid
Loading required package: plyr
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘trapezoid.Rnw’ failed with diagnostics:
 chunk 2 (label = trapezoid) 
Error in ggplot(data = data.frame(x, density), aes(x = x, y = density)) : 
  could not find function "ggplot"
Execution halted
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: ‘ggplot2’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Error: processing vignette ‘treecm.Rnw’ failed with diagnostics:
 chunk 14 (label = exStabilization5) 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘phyloseq’ ‘ggplot2’

Package suggested but not available for checking: ‘adaptiveGPCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘adegenet’ ‘adephylo’ ‘rgl’ ‘RLumShiny’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘datadr’ ‘ggplot2’

Package suggested but not available for checking: ‘dplyr’

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

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

Packages suggested but not available for checking:
  ‘ggplot2’ ‘lplyr’ ‘observer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggtern’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ez’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘hdrcde’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 13-16 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking:
  ‘dplyr’ ‘tibble’ ‘forecast’ ‘ggplot2’ ‘tsibble’ ‘tibbletime’
  ‘nycflights13’
Running examples in ‘tsbox-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ts_ts
> ### Title: Convert Everything to Everything
> ### Aliases: ts_ts ts_data.frame ts_ts ts_df ts_ts ts_data.table ts_ts
> ###   ts_dt ts_ts ts_tbl ts_ts ts_tibbletime ts_ts ts_timeSeries ts_ts
> ###   ts_ts ts_tsibble ts_ts ts_tslist ts_ts ts_xts ts_ts ts_zoo
> 
> ### ** Examples
> 
> 
> x.ts <- ts_c(mdeaths, fdeaths)
> head(x.ts)
     mdeaths fdeaths
[1,]    2134     901
[2,]    1863     689
[3,]    1877     827
[4,]    1877     677
[5,]    1492     522
[6,]    1249     406
> head(ts_df(x.ts))
       id       time value
1 mdeaths 1974-01-01  2134
2 mdeaths 1974-02-01  1863
3 mdeaths 1974-03-01  1877
4 mdeaths 1974-04-01  1877
5 mdeaths 1974-05-01  1492
6 mdeaths 1974-06-01  1249
> 
> suppressMessages(library(dplyr))
Error in library(dplyr) : there is no package called ‘dplyr’
Calls: suppressMessages -> withCallingHandlers -> library
Execution halted
Packages required but not available: ‘ICtest’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gcmr’
Error in re-building vignettes:
  ...
Loading required package: splines
Loading required package: gamlss.data
Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
 **********   GAMLSS Version 5.1-0  ********** 
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.

Loading required package: stats4
Loading required package: tseries
Loading required package: quantmod
Loading required package: xts
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: TTR

Attaching package: 'TTR'

The following object is masked from 'package:gamlss.dist':

    DPO

Version 0.4-0 included new data defaults. See ?getSymbols.
Warning in vglm.fitter(x = x, y = y, w = w, offset = offset, Xm2 = Xm2,  :
  iterations terminated because half-step sizes are very small
Warning in vglm.fitter(x = x, y = y, w = w, offset = offset, Xm2 = Xm2,  :
  some quantities such as z, residuals, SEs may be inaccurate due to convergence at a half-step

Error: processing vignette ‘tsglm.Rnw’ failed with diagnostics:
 chunk 42 (label = gcmr-package) 
Error in library("gcmr") : there is no package called 'gcmr'
Execution halted
Packages required but not available: ‘TSclust’ ‘longitudinalData’

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

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’ ‘tidyselect’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘hts’ ‘nycflights13’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 26-38 (TSrepr_extentions.Rmd) 
Error: processing vignette ‘TSrepr_extentions.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘bfast’ ‘broom’ ‘ggplot2’

Packages suggested but not available for checking: ‘rgl’ ‘car’

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

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘TSVC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TSVC
> ### Title: Tree-Structured Modelling of Varying Coefficients
> ### Aliases: TSVC print.TSVC
> 
> ### ** Examples
> 
> # Swiss Labour Market 
> library(AER)
Error in library(AER) : there is no package called ‘AER’
Execution halted
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <fig1>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 41-43 (example.Rmd) 
Error: processing vignette ‘example.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘mlrMBO’ ‘mlr’ ‘smoof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘streamR’ ‘ggmap’ ‘ggplot2’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_gpx
> ### Title: Read GPX file
> ### Aliases: read_gpx
> 
> ### ** Examples
> 
> ## for visualisation we are using mapview
> 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’
> ## assign  GPX file
> gpxFN <- system.file("extdata", "flighttrack.gpx", package = "uavRmp")
> 
> ## read it
> gpx <- read_gpx(gpxFN, layers=c("tracks"))
> 
> ## plot it
> mapview::mapview(gpx)
Error in loadNamespace(name) : there is no package called ‘mapview’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘ggmap’ ‘dplyr’ ‘ggplot2’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘UBL-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ImbC
> ### Title: Synthetic Imbalanced Data Set for a Multi-class Task
> ### Aliases: ImbC
> ### Keywords: datasets
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> data(ImbC)
> summary(ImbC)
       X1              X2         Class    
 Min.   :-13.5843   cat :300   normal:859  
 1st Qu.: -2.6930   dog :400   rare1 : 10  
 Median : -0.1592   fish:300   rare2 :131  
 Mean   : -0.1064                          
 3rd Qu.:  2.4633                          
 Max.   : 12.7836                          
> ggplot(data=ImbC, aes(x=X2, y=X1, color=Class))+geom_jitter()
Error in ggplot(data = ImbC, aes(x = X2, y = X1, color = Class)) : 
  could not find function "ggplot"
Execution halted
Packages required but not available: ‘ChemmineR’ ‘usethis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘ggplot2’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ukgasapi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dataItemExplorer
> ### Title: Data Item Explorer API
> ### Aliases: dataItemExplorer
> 
> ### ** Examples
> 
> # Specify the data item(s) to enquire from API
> dataitems <- c('Storage Injection, Actual',
+                'Storage Withdrawal, Actual')
> 
> # Initialise API (requires internet connection for this step)
> response <- dataItemExplorer(dataitems,
+                              fromdate = '2013-10-01',
+                              todate='2015-09-30')
*   Trying 40.127.139.252...
* TCP_NODELAY set
* Connected to marketinformation.natgrid.co.uk (40.127.139.252) port 80 (#0)
> POST /MIPIws-public/public/publicwebservice.asmx HTTP/1.1
Host: marketinformation.natgrid.co.uk
Accept: text/xml
Content-Type: application/soap+xml; charset=utf-8
Content-Length: 655

* upload completely sent off: 655 out of 655 bytes
< HTTP/1.1 200 OK
< Cache-Control: private, max-age=0
< Content-Length: 518779
< Content-Type: application/soap+xml; charset=utf-8
< Server: Microsoft-IIS/10.0
< X-AspNet-Version: 4.0.30319
< X-Powered-By: ASP.NET
< Set-Cookie: ARRAffinity=2f021e61b5e9da5f3dfd7fccb6ffa8f3d283638cc7b64973ed17bdbc4fd79d6f;Path=/;HttpOnly;Domain=marketinformation.natgrid.co.uk
< Date: Mon, 25 Jun 2018 17:02:50 GMT
< 
* Connection #0 to host marketinformation.natgrid.co.uk left intact
> 
> # Visualise the results on a chart
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘ggplot2’ ‘AdaptGauss’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cowplot’ ‘ggplot2’ ‘DiagrammeR’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘UncertainInterval-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nlopt.ui.general
> ### Title: Function for the determination of the population thresholds an
> ###   inconclusive interval for bi-normal distributed test scores.
> ### Aliases: nlopt.ui.general
> 
> ### ** Examples
> 
> # A simple test model:
> nlopt.ui.general(Se = .55, Sp = .55,
+                  distribution = 'norm',
+                  parameters.d0 = c(mean = 0, sd = 1),
+                  parameters.d1 = c(mean = 1, sd = 1),
+                  overlap.interval=c(-2,3))
$status
[1] 4

$message
[1] "NLOPT_XTOL_REACHED: Optimization stopped because xtol_rel or xtol_abs (above) was reached."

$intersection
[1] 0.5

$results
exp.Sp.ui exp.Se.ui      mean        sd      mean        sd 
     0.55      0.55      0.00      1.00      1.00      1.00 

$solution
         L          U 
0.09307899 0.90692101 

> # Standard procedure when using a continous distribution:
> nlopt.ui.general(parameters.d0 = c(mean = 0, sd = 1),
+                  parameters.d1 = c(mean = 1.6, sd = 2))
Warning in nlopt.ui.general(parameters.d0 = c(mean = 0, sd = 1), parameters.d1 = c(mean = 1.6,  :
  More than one point of intersection. Point with highest density used.
$status
[1] 4

$message
[1] "NLOPT_XTOL_REACHED: Optimization stopped because xtol_rel or xtol_abs (above) was reached."

$intersection
[1] 1.194722

$results
exp.Sp.ui exp.Se.ui      mean        sd      mean        sd 
     0.55      0.55      0.00      1.00      1.60      2.00 

$solution
        L         U 
0.9107232 1.5315608 

> emp.AUC <- function(norm, abnorm) {
+   o = outer(abnorm, norm, "-")
+   mean((o > 0) + .5 * (o == 0))
+ }
> 
> library(MASS)
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 161-169 (UI-vignette.Rmd) 
Error: processing vignette ‘UI-vignette.Rmd’ failed with diagnostics:
there is no package called 'car'
Execution halted
Packages suggested but not available for checking: ‘tibble’ ‘ggforce’
Running ‘plot.R’ [1s/1s]
  Running ‘set_units.R’ [0s/1s]
  Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(units)
  udunits system database from /usr/share/xml/udunits
  > 
  > test_check("units")
  ── 1. Error: type_sum is available for units objects (@test_misc.R#37)  ────────
  there is no package called 'tibble'
  1: library(tibble) at testthat/test_misc.R:37
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 288 SKIPPED: 3 FAILED: 1
  1. Error: type_sum is available for units objects (@test_misc.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Error : cannot convert cm*km/h/s into cm/s
Quitting from lines 384-387 (measurement_units_in_R.Rmd) 
Error: processing vignette ‘measurement_units_in_R.Rmd’ failed with diagnostics:
there is no package called 'ggforce'
Execution halted
Packages required but not available: ‘dplyr’ ‘tibble’

Packages suggested but not available for checking: ‘gapminder’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘dtplyr’ ‘purrr’ ‘tidyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘readxl’ ‘tidyr’ ‘ggplot2’
Running examples in ‘unvotes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: un_roll_calls
> ### Title: Data on each roll call of the United Nations General Assembly
> ### Aliases: un_roll_calls
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 24-28 (unvotes.Rmd) 
Error: processing vignette ‘unvotes.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking:
  ‘USAboundariesData’ ‘dplyr’ ‘leaflet’
Error in re-building vignettes:
  ...
Quitting from lines 23-30 (usaboundaries-sample-analysis.Rmd) 
Error: processing vignette ‘usaboundaries-sample-analysis.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘purrr’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘car’ ‘data.tree’ ‘DiagrammeR’ ‘GGally’ ‘ggplot2’ ‘ggrepel’
  ‘ggridges’ ‘rio’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rematch2’ ‘styler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘usmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_usmap
> ### Title: Conveniently plot basic US map
> ### Aliases: plot_usmap
> 
> ### ** Examples
> 
> plot_usmap()
Error in plot_usmap() : 
  Please install `ggplot2`. Use: install.packages("ggplot2")
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(usmap)
  > 
  > test_check("usmap")
  ── 1. Error: (unknown) (@test-plot.R#10)  ──────────────────────────────────────
  Please install `ggplot2`. Use: install.packages("ggplot2")
  1: plot_usmap() at testthat/test-plot.R:10
  2: stop("Please install `ggplot2`. Use: install.packages(\"ggplot2\")")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 59 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-plot.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 21-22 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
Please install `ggplot2`. Use: install.packages("ggplot2")
Execution halted
Packages suggested but not available for checking:
  ‘vaers’ ‘vaersND’ ‘dplyr’
Packages required but not available:
  ‘dplyr’ ‘readr’ ‘tibble’ ‘broom’ ‘ggplot2’

Packages suggested but not available for checking:
  ‘purrr’ ‘tidyr’ ‘DT’ ‘cowplot’ ‘dbplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cowplot’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 80-92 (varrank.Rmd) 
Error: processing vignette ‘varrank.Rmd’ failed with diagnostics:
there is no package called 'caret'
Execution halted
Running examples in ‘VARSEDIG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VARSEDIG
> ### Title: Variable selection to discriminate among taxonomic groups
> ### Aliases: VARSEDIG
> ### Keywords: VARSEDIG
> 
> ### ** Examples
> 
> 
> data(characiformes)
> 
> VARSEDIG(data = characiformes , variables = c("M2","M3","M4","M5","M6","M7","M8","M9","M10",
+ "M11","M12","M13","M14","M15","M16","M17","M18","M19","M20","M21","M22","M23",
+ "M24","M25","M26","M27","M28"), group="Species" , group1= "Moenkhausia oligolepis",
+ group2="Moenkhausia dichroura", LEGENDd=c("x='topright'", "legend = dati",
+ "col = COLORB", "lty=lty", "bty='n'", "cex=1.2", "text.font= 3"),
+ LEGENDs=c("x='topright'", "legend=unique(datosF[,'Group'])", "col = color1",
+ "pch = pcht", "bty='n'", "cex=1.2", "text.font=3"), LEGENDr=c("x='topright'",
+ "legend = dati", "col=col", "pch= c(16,16)", "bty='n'", "cex=1.2", "text.font=3"),
+ XLIMs=c(-1.2,1.2), YLIMs=c(-1.3,1.3), BIVTEST12=c("br=br", "cex=1.1",
+ "col=colbiv", "sub=sub", "Pcol=Pcol"), BIVTEST21=c("br=br", "cex=1.1",
+ "col=colbiv", "sub=sub", "Pcol=Pcol"), colbiv="blue")
dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
dev.new(): using pdf(file="Rplots3.pdf")
Error in loadNamespace(name) : there is no package called ‘car’
Calls: VARSEDIG ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘car’ ‘rgl’ ‘AER’
Error in re-building vignettes:
  ...
Loading required package: vcd
Loading required package: grid
Loading required package: gnm

Error: processing vignette ‘vcd-tutorial.Rnw’ failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘dplyr’ ‘tibble’

Packages suggested but not available for checking:
  ‘adegenet’ ‘ggplot2’ ‘poppr’ ‘tidyr’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GGally’ ‘dplyr’ ‘broom’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘lmerTest’

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

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

Package suggested but not available for checking: ‘dplyr’

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

Packages suggested but not available for checking:
  ‘ggplot2’ ‘tidyr’ ‘dplyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘ggbeeswarm’
Error in re-building vignettes:
  ...
Loading required package: sm
Package 'sm', version 2.2-5.5: type help(sm) for summary information

Error: processing vignette ‘methodComparison.Rnw’ failed with diagnostics:
 chunk 18 (label = showDiamond) 
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘pdp’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘viridisLite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: viridis
> ### Title: Matplotlib 'viridis' and 'cividis' color map
> ### Aliases: viridis viridisMap magma inferno plasma cividis
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘ggplot2’ ‘tidyr’ ‘dplyr’ ‘purrr’

Packages suggested but not available for checking: ‘plotly’ ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘colourpicker’ ‘ggraph’
Packages required but not available: ‘ggplot2’ ‘readxl’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘vlad-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calceo
> ### Title: Compute Expected minus Observed value
> ### Aliases: calceo
> ### Keywords: keyword1 keyword2
> 
> ### ** Examples
> 
> library("vlad")
> # see Steiner (2014) p. 234
> coeff <- c("(Intercept)"=-3.68, "Parsonnet"=0.077)
> # penalty reward for death (E-O scores multiplied with -1 to get O-E scores)
> calceo(df=data.frame(as.integer(0), 1), coeff=coeff)*-1
[1] 0.9753976
> calceo(df=data.frame(as.integer(50), 1), coeff=coeff)*-1
[1] 0.4576021
> # penalty reward for survival
> calceo(df=data.frame(as.integer(0), 0), coeff=coeff)*-1
[1] -0.02460243
> calceo(df=data.frame(as.integer(50), 0), coeff=coeff)*-1
[1] -0.5423979
> 
> # Plot a VLAD/CRAM chart
> library("spcadjust")
> data("cardiacsurgery")
> cardiacsurgery <- dplyr::mutate(cardiacsurgery, phase=factor(ifelse(date < 2*365, "I", "II")))
Error in loadNamespace(name) : there is no package called ‘dplyr’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘ggmap’ ‘marmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘lmerTest’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘VoxR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VoxR-package
> ### Title: Metrics extraction of trees from T-LiDAR data
> ### Aliases: VoxR-package VoxR
> ### Keywords: package 3d point cloud LiDAR
> 
> ### ** Examples
> 
> data(treecloud)
> 
> #-voxelisation using the vox function
> 
> treecloud_vox <- vox(treecloud,res=0.02)
> 
> #-visualisation
> 
> require(rgl)
Loading required package: rgl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgl’
> library(rgl)
Error in library(rgl) : there is no package called ‘rgl’
Execution halted
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘viridis’ ‘ggplot2’

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

Package suggested but not available for checking: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: rquery
Quitting from lines 35-60 (vtreatRareLevels.Rmd) 
Error: processing vignette ‘vtreatRareLevels.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘bayesplot’ ‘rstan’ ‘dplyr’ ‘ggplot2’

Package suggested but not available for checking: ‘diagis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘shinystan’

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

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

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

Packages suggested but not available for checking: ‘ggplot2’ ‘Rraven’

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

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [14s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(wdm)
  > 
  > test_check("wdm")
  ── 1. Error: method hoeffding is correct (@test_computations_unweighted.R#24)  ─
  there is no package called 'Hmisc'
  1: expect_equal(wdm(x, method = "hoeffd"), Hmisc::hoeffd(x)$D) at testthat/test_computations_unweighted.R:24
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: Hmisc::hoeffd
  5: getExportedValue(pkg, name)
  6: asNamespace(ns)
  7: getNamespace(ns)
  8: tryCatch(loadNamespace(name), error = function(e) stop(e))
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: value[[3L]](cond)
  
  ── 2. Error: method hoeffding is correct (@test_computations_unweighted.R#79)  ─
  there is no package called 'Hmisc'
  1: expect_equal(indep_test(x, y, method = "hoeffd")$p_value, Hmisc::hoeffd(x, y)$P[1, 
         2], tol = 0.03) at testthat/test_computations_unweighted.R:79
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: Hmisc::hoeffd
  5: getExportedValue(pkg, name)
  6: asNamespace(ns)
  7: getNamespace(ns)
  8: tryCatch(loadNamespace(name), error = function(e) stop(e))
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 73 SKIPPED: 0 FAILED: 2
  1. Error: method hoeffding is correct (@test_computations_unweighted.R#24) 
  2. Error: method hoeffding is correct (@test_computations_unweighted.R#79) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘ggmap’

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

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

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

Package suggested but not available for checking: ‘jtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘wellknown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multilinestring
> ### Title: Make WKT multilinestring objects
> ### Aliases: multilinestring
> 
> ### ** Examples
> 
> ## empty multilinestring
> multilinestring("empty")
[1] "MULTILINESTRING EMPTY"
> # multilinestring("stuff")
> 
> # character string
> x <- "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> multilinestring(x)
[1] "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> 
> # data.frame
> df <- data.frame(long = c(30, 45, 10), lat = c(20, 40, 40))
> df2 <- data.frame(long = c(15, 40, 10), lat = c(5, 10, 20))
> multilinestring(df, df2, fmt=0)
[1] "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> lint(multilinestring(df, df2, fmt=0))
[1] TRUE
> wktview(multilinestring(df, df2), zoom=3)
Error: Please install leaflet
Execution halted
Package required but not available: ‘NPflow’

Package suggested but not available for checking: ‘EdSurvey’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘tidytext’ ‘purrr’ ‘broom’

Packages suggested but not available for checking:
  ‘ggraph’ ‘gapminder’ ‘fuzzyjoin’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘rgl’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dbplyr’ ‘dplyr’ ‘purrr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘ggplot2’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘readxl’ ‘nycflights13’
Running examples in ‘writexl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write_xlsx
> ### Title: Export to xlsx
> ### Aliases: write_xlsx writexl
> 
> ### ** Examples
> 
> # Roundtrip example
> tmp <- write_xlsx(iris)
> readxl::read_xlsx(tmp)
Error in loadNamespace(name) : there is no package called ‘readxl’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running ‘spelling.R’ [1s/1s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(writexl)
  > 
  > test_check("writexl")
  ── 1. Error: Performance is OK (@test-performance.R#4)  ────────────────────────
  there is no package called 'nycflights13'
  1: writexl::write_xlsx(nycflights13::flights) at testthat/test-performance.R:4
  2: is.data.frame(x)
  3: nycflights13::flights
  4: getExportedValue(pkg, name)
  5: asNamespace(ns)
  6: getNamespace(ns)
  7: tryCatch(loadNamespace(name), error = function(e) stop(e))
  8: tryCatchList(expr, classes, parentenv, handlers)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: value[[3L]](cond)
  
  ── 2. Error: Types roundtrip properly (@test-types.R#14)  ──────────────────────
  there is no package called 'readxl'
  1: expect_equal(df, as.data.frame(roundtrip(df))) at testthat/test-types.R:14
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: as.data.frame(roundtrip(df))
  5: roundtrip(df)
  6: readxl::read_xlsx at testthat/test-types.R:4
  7: getExportedValue(pkg, name)
  8: asNamespace(ns)
  9: getNamespace(ns)
  10: tryCatch(loadNamespace(name), error = function(e) stop(e))
  11: tryCatchList(expr, classes, parentenv, handlers)
  12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  13: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 2
  1. Error: Performance is OK (@test-performance.R#4) 
  2. Error: Types roundtrip properly (@test-types.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘car’ ‘mediation’
Error in re-building vignettes:
  ...
Quitting from lines 951-952 (WRS2.Rnw) 
Error: processing vignette ‘WRS2.Rnw’ failed with diagnostics:
there is no package called 'mediation'
Execution halted
Packages required but not available: ‘Hmisc’ ‘ggplot2’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘caret’ ‘dplyr’ ‘EnvStats’ ‘forecast’ ‘purrr’ ‘tidyr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘bupaR’ ‘dplyr’ ‘tidyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘DiagrammeR’
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘ggrepel’ ‘ggnetwork’

Packages suggested but not available for checking:
  ‘treemapify’ ‘ggraph’ ‘ggbio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: XLConnect
Loading required package: XLConnectJars
XLConnect 0.2-15 by Mirai Solutions GmbH [aut],
  Martin Studer [cre],
  The Apache Software Foundation [ctb, cph] (Apache POI),
  Graph Builder [ctb, cph] (Curvesapi Java library)
http://www.mirai-solutions.com
https://github.com/miraisolutions/xlconnect
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.poi.util.DocumentHelper (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/XLConnect/java/poi-ooxml-3.17.jar) to method com.sun.org.apache.xerces.internal.util.SecurityManager.setEntityExpansionLimit(int)
WARNING: Please consider reporting this to the maintainers of org.apache.poi.util.DocumentHelper
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘XLConnect.Rnw’ failed with diagnostics:
 chunk 20 (label = AdvancedExampleP5) 
Error in ggplot(gcurr, aes(Date, Value, colour = Currency)) : 
  could not find function "ggplot"
Execution halted
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘car’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘ggforce’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’ ‘vpc’

Package suggested but not available for checking: ‘plotly’

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

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

Packages suggested but not available for checking: ‘DT’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘tibble’ ‘tidyr’ ‘pROC’ ‘tidyselect’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DT’ ‘ggplot2’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggetho’ ‘damr’
Packages required but not available: ‘dplyr’ ‘Zelig’

Package suggested but not available for checking: ‘zeligverse’

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

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

Packages suggested but not available for checking:
  ‘tidyverse’ ‘ZeligChoice’ ‘ZeligEI’ ‘zeligverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘tibble’ ‘WhatIf’ ‘Zelig’ ‘ZeligChoice’ ‘ZeligEI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: TSP
Loading required package: gtools
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: grid
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 160-190 (selected_features.Rmd) 
Error: processing vignette ‘selected_features.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘tidyr’ ‘ggplot2’ ‘tibble’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘zdat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘geomorph’ ‘ggplot2’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘zoocat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gmon_trans
> ### Title: Tools for plottin 'zoocat' objects with ggplot2
> ### Aliases: gmon_trans scale_x_gmon scale_y_gmon
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘rfigshare’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rARPACK’ ‘sparseLDA’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘AdaptFit/R/aspm.R’:
  assign("group.vec.Handan", group.vec, pos = 1)
  assign("X.Declan", X, pos = 1)
  assign("Z.Jaida", Z, pos = 1)
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rjson’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Namespace in Imports field not imported from: ‘unmarked’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘gridExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘magrittr’
  All declared Imports should be used.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rgdal’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
Namespace in Imports field not imported from: ‘caret’
  All declared Imports should be used.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/aqr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.6Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
File ‘audio/libs/audio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘jsonlite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
    libs   2.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is 103.4Mb
  sub-directories of 1Mb or more:
    libs  102.6Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.7Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  16.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.0Mb
    libs   3.6Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 58.0Mb
  sub-directories of 1Mb or more:
    libs  57.2Mb
Namespace in Imports field not imported from: ‘inline’
  All declared Imports should be used.
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  24.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   3.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
installed size is 92.2Mb
  sub-directories of 1Mb or more:
    libs  92.1Mb
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.2Mb
Namespace in Imports field not imported from: ‘readxl’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 98.2Mb
  sub-directories of 1Mb or more:
    libs  96.8Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crochet’
  All declared Imports should be used.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
installed size is 144.8Mb
  sub-directories of 1Mb or more:
    include  144.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.0Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lattice’ ‘zoo’
  All declared Imports should be used.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   8.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Package suggested but not available for checking: ‘RQuantLib’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RGtk2’ ‘cairoDevice’ ‘ergm’ ‘foreign’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘haven’ ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘blkergm’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘blkergm’
See ‘/data/gannet/ripley/R/packages/tests-clang/blkergm.Rcheck/00install.out’ for details.
installed size is 43.7Mb
  sub-directories of 1Mb or more:
    libs  42.6Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Namespace in Imports field not imported from: ‘descriptr’
  All declared Imports should be used.
Running examples in ‘blscrapeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: qcew_api
> ### Title: Request data from the Quarterly Census of Employment and Wages.
> ### Aliases: qcew_api
> ### Keywords: api bls cpi economics inflation unemployment
> 
> ### ** Examples
> 
> 
> # A request for the employment levels and wages for NIACS 5112: Software Publishers.
> dat <- qcew_api(year=2015, qtr="A", slice="area", sliceCode="US000")
Please set a numeric year.
Trying BLS servers...
URL caused a warning. Please check your parameters and try again: https://data.bls.gov/cew/data/api/2015/A/area/US000.csv
Error in qcew_api(year = 2015, qtr = "A", slice = "area", sliceCode = "US000") : 
  object 'qcewDat' not found
Execution halted
Namespace in Imports field not imported from: ‘plm’
  All declared Imports should be used.
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Found the following significant warnings:
  conditional.least.squares.c:232:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:233:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:234:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/bnlearn.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘yaml’
  All declared Imports should be used.
installed size is 376.8Mb
  sub-directories of 1Mb or more:
    include    3.2Mb
    lib      373.3Mb
installed size is 84.6Mb
  sub-directories of 1Mb or more:
    libs  84.1Mb
Error in re-building vignettes:
  ...
Quitting from lines 92-93 (bossa-refpkg.Rmd) 
Error: processing vignette 'bossa-refpkg.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
Execution halted
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘tidyr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  29.7Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R     3.5Mb
    doc   2.4Mb
Found the following significant warnings:

  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'ergm.update.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'ergm.update.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'ergm.update.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'ergm.update.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'ergm.update.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'ergm.update.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    bin    2.3Mb
    doc    1.1Mb
    libs   2.3Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  helpers.c:365:19: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BSquare.Rcheck/00install.out’ for details.
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
installed size is 98.7Mb
  sub-directories of 1Mb or more:
    libs  98.1Mb
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘btergm’
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘btergm’
See ‘/data/gannet/ripley/R/packages/tests-clang/btergm.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'ergm.update.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'ergm.update.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'ergm.update.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   3.3Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cowplot’ ‘dplyr’ ‘ranger’ ‘rms’ ‘survival’ ‘tidyverse’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Found the following significant warnings:
  slpcovis.cpp:381:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/catlearn.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
ConstructModel: warning in AddDynamicRegression(ss, formula, data =
  data, sigma.mean.prior = sigma.mean.prior): partial argument match of
  'sigma.mean.prior' to 'sigma.mean.prior.DEPRECATED'
Namespace in Imports field not imported from: ‘prettydoc’
  All declared Imports should be used.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘plot’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘plot’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/CCMnet.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘purrr’ ‘roxygen2’
  All declared Imports should be used.
Running examples in ‘CDECRetrieve-Ex.R’ failed
The error most likely occurred in:

> ### Name: cdec_rt
> ### Title: Get a rating table
> ### Aliases: cdec_rt
> 
> ### ** Examples
> 
> cdec_rt("abj") # get the stage to rating curve for ABJ
Error in open.connection(x, "rb") : 
  Timeout was reached: Connection timed out after 10000 milliseconds
Calls: cdec_rt ... %in% -> cdec_rt_list -> <Anonymous> -> read_html.default
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 55-69 (CDECRetrieve.Rmd) 
Error: processing vignette 'CDECRetrieve.Rmd' failed with diagnostics:
Timeout was reached: Connection timed out after 10000 milliseconds
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.8Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/changepoint.np.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘foreach’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tools’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Files which contain pragma(s) suppressing diagnostics:
  ‘src/cld_3/protos/feature_extractor.pb.h’
  ‘src/cld_3/protos/sentence.pb.h’ ‘src/cld_3/protos/task_spec.pb.h’
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  ./networkCliqueMSR.h:4:9: warning: 'NETWORKClIQUEMSR_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/data/gannet/ripley/R/packages/tests-clang/cliqueMS.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘infuser’ ‘purrr’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data     3.5Mb
    exdata   5.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘graphics’ ‘htmltools’ ‘pander’ ‘readr’
  All declared Imports should be used.
Running examples in ‘codebook-Ex.R’ failed
The error most likely occurred in:

> ### Name: codebook_missingness
> ### Title: Codebook missingness
> ### Aliases: codebook_missingness
> 
> ### ** Examples
> 
> data("bfi")
> codebook_missingness(bfi)
Error in `rownames<-`(`*tmp*`, value = table(pat)) : 
  attempt to set 'rownames' on an object with no dimensions
Calls: codebook_missingness -> md_pattern -> <Anonymous> -> rownames<-
Execution halted
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘geometry’ ‘parallel’ ‘plot3D’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘flashClust’ ‘speedglm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rscala’
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/CompRandFld.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘MASS’ ‘geepack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
Namespaces in Imports field not imported from:
  ‘Rtsne’ ‘scatterplot3d’
  All declared Imports should be used.
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.5Mb
Namespace in Imports field not imported from: ‘xtable’
  All declared Imports should be used.
Package in Depends field not imported from: ‘calibrate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.2Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 38.8Mb
  sub-directories of 1Mb or more:
    libs  38.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
QR.cd: no visible global function definition for ‘quantile’
QR.lasso.cd: no visible global function definition for ‘quantile’
cqr.cd: no visible global function definition for ‘quantile’
cqr.lasso.cd: no visible global function definition for ‘quantile’
cqr.lasso.mm: no visible global function definition for ‘quantile’
cqr.mm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘AnnotationDbi’ ‘clusterProfiler’ ‘org.Hs.eg.db’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Namespace in Imports field not imported from: ‘httpcode’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
Note: found 59670 marked Latin-1 strings
  Note: found 16 marked UTF-8 strings
Found the following significant warnings:
  ./ctl.h:38:23: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
  ./ctl.h:36:25: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
See ‘/data/gannet/ripley/R/packages/tests-clang/ctl.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘tea’
  All declared Imports should be used.
installed size is 74.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    doc    4.1Mb
    libs  64.0Mb
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    extdata  31.9Mb
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   5.1Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘Demerelate’ ‘misc3d’ ‘plotly’ ‘quadprog’ ‘rgl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    java  15.2Mb
Namespaces in Imports field not imported from:
  ‘DatabaseConnectorJars’ ‘bit’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
.onLoad : <anonymous>: no visible global function definition for
  ‘read.table’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbConnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbListTables’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbExistsTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbReadTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbWriteTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbDisconnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbRemoveTable’
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is 61.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  59.3Mb
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
browse: no visible global function definition for ‘slot’
browse: no visible global function definition for ‘page’
default.options: no visible binding for global variable ‘object.size’
heat.view: no visible global function definition for ‘head’
heat.view: no visible global function definition for ‘tail’
whos: no visible global function definition for ‘slotNames’
whos : <anonymous> : <anonymous>: no visible global function definition
  for ‘slot’
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘gridExtra’ ‘latticeExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘CDM’
  All declared Imports should be used.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
Namespace in Imports field not imported from: ‘oz’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘UScensus2010’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Bootstrapping.CI: no visible global function definition for ‘quantile’
D.Jost: no visible global function definition for ‘read.table’
D.Jost: no visible global function definition for ‘write.table’
Dv.locis.corrected.calc: no visible global function definition for
  ‘p.adjust’
Gst.Nei: no visible global function definition for ‘read.table’
Gst.Nei: no visible global function definition for ‘write.table’
H.out: no visible global function definition for ‘write.table’
Hardy.calc: no visible global function definition for ‘chisq.test’
critical.ci.values: no visible global function definition for
  ‘quantile’
inputformat: no visible global function definition for ‘read.table’
inputformat: no visible global function definition for ‘write.table’
over.all.pops: no visible global function definition for ‘write.table’
p.value.correcture: no visible global function definition for
  ‘p.adjust’
pair.pops: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Found the following significant warnings:
  DEploid/updateHap.cpp:670:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:678:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:681:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:682:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/DEploid.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.4Mb
    libs   1.6Mb
Packages which this enhances but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rmosek’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  45.9Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  17.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  16.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   2.8Mb
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   5.8Mb
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Namespaces in Imports field not imported from:
  ‘bit64’ ‘rstudioapi’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Found the following significant warnings:
  compnoreggilks.cpp:31:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compnoreggilks.cpp:90:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:32:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:88:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:150:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:207:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:380:8: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/DPWeibull.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘shapefiles’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.1Mb
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  21.0Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’ ‘scales’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘base64enc’ ‘knitr’ ‘markdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.2Mb
installed size is 53.9Mb
  sub-directories of 1Mb or more:
    libs  53.2Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Namespaces in Imports field not imported from:
  ‘graphics’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    xsd   5.4Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Namespaces in Imports field not imported from:
  ‘BiocParallel’ ‘broom’ ‘reshape2’ ‘rmarkdown’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    3.3Mb
    help   3.4Mb
Found the following significant warnings:
  input2.c:767:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/epanet2toolkit.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘ROCR’ ‘c060’ ‘methods’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘llogistic’ ‘logitnorm’
  All declared Imports should be used.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/Equalden.HD.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.count’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.count’
See ‘/data/gannet/ripley/R/packages/tests-clang/ergm.count.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘ergm::colMeans.mcmc.list’ by ‘statnet.common::colMeans.mcmc.list’ when loading ‘ergm.ego’
  Warning: replacing previous import ‘ergm::sweep.mcmc.list’ by ‘statnet.common::sweep.mcmc.list’ when loading ‘ergm.ego’
See ‘/data/gannet/ripley/R/packages/tests-clang/ergm.ego.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.graphlets’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.graphlets’
See ‘/data/gannet/ripley/R/packages/tests-clang/ergm.graphlets.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.rank’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.rank’
See ‘/data/gannet/ripley/R/packages/tests-clang/ergm.rank.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.userterms’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.userterms’
See ‘/data/gannet/ripley/R/packages/tests-clang/ergm.userterms.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'ergm.update.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘searcher’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘modelr’
  All declared Imports should be used.
Running ‘testthat.R’ [7s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ess)
  > 
  > test_check("ess")
  ── 1. Failure: show_country_rounds returns correct rounds for countries (@test-s
  show_country_rounds("Italy") not equal to c(1, 2, 6).
  Lengths differ: 4 is not 3
  
  ── 2. Failure: show_country_rounds returns correct rounds for countries (@test-s
  show_country_rounds("Spain") not equal to 1:7.
  Lengths differ: 8 is not 7
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 36 SKIPPED: 23 FAILED: 2
  1. Failure: show_country_rounds returns correct rounds for countries (@test-show_.R#100) 
  2. Failure: show_country_rounds returns correct rounds for countries (@test-show_.R#101) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘msm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘CodeDepends’ ‘DT’ ‘PKI’ ‘shinycssloaders’ ‘tictoc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Namespace in Imports field not imported from: ‘refund’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forcats’ ‘formula.tools’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.1Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-clang/FastRWeb.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 53.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  50.6Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   7.1Mb
Namespaces in Imports field not imported from:
  ‘cellranger’ ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Found the following significant warnings:
  ff.cpp:256:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ff.cpp:256:54: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/ff.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Namespace in Imports field not imported from: ‘desc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Namespaces in Imports field not imported from:
  ‘base’ ‘pbapply’ ‘stringr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/freetypeharfbuzz.Rcheck/00install.out’ for details.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package suggested but not available for checking: ‘dggrids’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.8Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘grDevices’ ‘graphics’ ‘matrixStats’ ‘stats’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   8.6Mb
installed size is 63.1Mb
  sub-directories of 1Mb or more:
    libs  62.7Mb
installed size is 77.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     73.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘roxygen2’ ‘testthat’ ‘utils’ ‘withr’
  All declared Imports should be used.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  16.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/gdmp.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NMF’ ‘RColorBrewer’ ‘VennDiagram’ ‘clValid’ ‘data.table’ ‘grid’
  ‘gtools’ ‘pca3d’ ‘rmarkdown’ ‘scales’ ‘shinydashboard’ ‘shinyjs’
  ‘statmod’ ‘stringr’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    exdata   5.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs   3.7Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         3.5Mb
    extdata   1.4Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  12.3Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘utils’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
Found the following significant warnings:
  FORCE_certify.c:116:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/GFORCE.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggforce’ ‘plyr’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Namespaces in Imports field not imported from:
  ‘GGEBiplotGUI’ ‘gge’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
Found the following significant warnings:

  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
  Warning: 'as.units' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridGraphics’ ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘XML’ ‘mapproj’ ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHANES’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘colourpicker’ ‘dplyr’ ‘ggrepel’ ‘grDevices’ ‘gridExtra’
  ‘lazyeval’ ‘markdown’ ‘plotly’ ‘quantreg’ ‘rlang’ ‘shinyjs’ ‘tidyr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.1Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘GGally’ ‘RColorBrewer’ ‘Rcpp’ ‘assertthat’ ‘backports’
  ‘colorspace’ ‘colourpicker’ ‘evaluate’ ‘futile.options’ ‘gdtools’
  ‘gtable’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘labeling’ ‘lambda.r’
  ‘lazyeval’ ‘magrittr’ ‘miniUI’ ‘munsell’ ‘plyr’ ‘reshape’ ‘rprojroot’
  ‘scales’ ‘stringi’ ‘stringr’ ‘svglite’ ‘tibble’ ‘xtable’ ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    libs  50.2Mb
installed size is 47.5Mb
  sub-directories of 1Mb or more:
    libs  46.3Mb
Package suggested but not available for checking: ‘cplexAPI’
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/gnmf.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘car’ ‘wordcloud’
  All declared Imports should be used.
Running examples in ‘gpg-Ex.R’ failed
The error most likely occurred in:

> ### Name: gpg_sign
> ### Title: PGP Signatures
> ### Aliases: gpg_sign gpg_verify gpg gpg_sign
> 
> ### ** Examples
> 
> # This requires you have the Debian master key in your keyring
> msg <- tempfile()
> sig <- tempfile()
> download.file("http://http.us.debian.org/debian/dists/jessie/Release", msg)
trying URL 'http://http.us.debian.org/debian/dists/jessie/Release'
Content type 'application/octet-stream' length 148406 bytes (144 KB)
==================================================
downloaded 144 KB

> download.file("http://http.us.debian.org/debian/dists/jessie/Release.gpg", sig)
trying URL 'http://http.us.debian.org/debian/dists/jessie/Release.gpg'
Content type 'application/octet-stream' length 2434 bytes
==================================================
downloaded 2434 bytes

> gpg_verify(sig, msg, error = FALSE)
Error: GnuPG detached verification error: General error
Execution halted
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    R  19.3Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘raster’ ‘rgeos’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘deldir’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Namespace in Imports field not imported from: ‘rrcov’
  All declared Imports should be used.
Running examples in ‘GuardianR-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_guardian
> ### Title: Search Guardian API for news articles that match the criteria
> ### Aliases: get_guardian
> ### Keywords: IO utilities
> 
> ### ** Examples
> 
> ## Not run:
> results <- get_guardian("islamic+state", 
+ 	section="world",
+ 	from.date="2014-09-16", 
+ 	to.date="2014-09-16", 
+ 	api.key="3xzg2fk53jcdgaj5tbwqqhcz")
Error in get_json(keywords, section, format, from.date, to.date, api.key) : 
  !is.null(this.api.response) is not TRUE
Calls: get_guardian -> get_json -> stopifnot
Execution halted
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘methods’
  All declared Imports should be used.
installed size is 145.9Mb
  sub-directories of 1Mb or more:
    java  144.1Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following significant warnings:
  SNPHWEX.cpp:50:31: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  SNPHWEX.cpp:51:65: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/HardyWeinberg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./City.h:82:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:93:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:94:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:95:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:96:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:87:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:89:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:267:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:268:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ./Spooky.h:285:36: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashFunction.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ../inst/include/hashmap/sparsepp/spp.h:2342:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/hashmap/sparsepp/spp.h:2365:22: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashmap.Rcheck/00install.out’ for details.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
Running ‘testthat.R’ [9m/13m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(healthcareai)
  healthcareai version 2.0.0
  Please visit https://docs.healthcare.ai for full documentation and vignettes. Join the community at https://healthcare-ai.slack.com
  > Sys.setenv("R_TESTS" = "")
  > test_check("healthcareai")
  ── 1. Failure: dummy columns are created as expected (@test-prep_data.R#278)  ──
  all(n == exp) isn't true.
  
  ── 2. Failure: prep_data respects add_levels = FALSE (@test-prep_data.R#428)  ──
  any(c("other", "missing") %in% levels(pd$x)) isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 728 SKIPPED: 7 FAILED: 2
  1. Failure: dummy columns are created as expected (@test-prep_data.R#278) 
  2. Failure: prep_data respects add_levels = FALSE (@test-prep_data.R#428) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘memoise’ ‘ratelimitr’
  All declared Imports should be used.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc          13.7Mb
    htmlwidgets   1.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        7.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   2.5Mb
Found the following significant warnings:
  language.c:41:5: warning: flexible array initialization is a GNU extension [-Wgnu-flexible-array-initializer]
See ‘/data/gannet/ripley/R/packages/tests-clang/htmltidy.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    data  12.8Mb
    doc    1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   4.6Mb
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'lo' to 'locut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'hi' to 'hicut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘ggplot2’ ‘pander’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.2Mb
Found the following significant warnings:
  IBDsim.c:27:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:39:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:54:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:61:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/IBDsim.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    R     14.5Mb
    doc    5.9Mb
    libs  13.5Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.1Mb
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs  35.4Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  24.1Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.0Mb
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     30.7Mb
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
Running examples in ‘imfr-Ex.R’ failed
The error most likely occurred in:

> ### Name: imf_codes
> ### Title: Retrieve individual database codes
> ### Aliases: imf_codes
> 
> ### ** Examples
> 
> # Retrieve indicators from BOP database
> test = imf_codes(codelist = 'CL_INDICATOR_BOP')

Downloading: 1.2 kB     
Downloading: 1.2 kB     
Downloading: 3.8 kB     
Downloading: 3.8 kB     
Downloading: 3.8 kB     
Downloading: 3.8 kB     
Downloading: 3.8 kB     
Downloading: 3.8 kB     
Downloading: 4.1 kB     
Downloading: 4.1 kB     
Downloading: 13 kB     
Downloading: 13 kB     
Downloading: 13 kB     
Downloading: 13 kB     
Downloading: 30 kB     
Downloading: 30 kB     
Downloading: 30 kB     
Downloading: 30 kB     
Downloading: 31 kB     
Downloading: 31 kB     
Downloading: 48 kB     
Downloading: 48 kB     
Downloading: 54 kB     
Downloading: 54 kB     
Downloading: 56 kB     
Downloading: 56 kB     
Downloading: 63 kB     
Downloading: 63 kB     
Downloading: 65 kB     
Downloading: 65 kB     
Downloading: 67 kB     
Downloading: 67 kB     
Downloading: 83 kB     
Downloading: 83 kB     
Downloading: 100 kB     
Downloading: 100 kB     
Downloading: 120 kB     
Downloading: 120 kB     
Downloading: 130 kB     
Downloading: 130 kB     
Downloading: 130 kB     
Downloading: 130 kB     
Downloading: 140 kB     
Downloading: 140 kB     
Downloading: 150 kB     
Downloading: 150 kB     
Downloading: 150 kB     
Downloading: 150 kB     
Downloading: 150 kB     
Downloading: 150 kB     
Downloading: 150 kB     
Downloading: 150 kB     Error: Unable to download series.
Execution halted
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘vdiffr’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Namespace in Imports field not imported from: ‘prodlim’
  All declared Imports should be used.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   7.5Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.4Mb
Namespace in Imports field not imported from: ‘irr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘animation’ ‘comtradr’ ‘ndtv’ ‘statnet’ ‘xergm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘lubridate’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fAssets’ ‘timeDate’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’
  ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.7Mb
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      4.5Mb
Namespace in Imports field not imported from: ‘mclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stinepack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EQL’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   8.2Mb
Namespaces in Imports field not imported from:
  ‘nleqslv’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R   4.8Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.7Mb
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  'dim' to 'dims'
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/LambertW.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘repr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import ‘ergm::colMeans.mcmc.list’ by ‘statnet.common::colMeans.mcmc.list’ when loading ‘latentnet’
  Warning: replacing previous import ‘ergm::sweep.mcmc.list’ by ‘statnet.common::sweep.mcmc.list’ when loading ‘latentnet’
See ‘/data/gannet/ripley/R/packages/tests-clang/latentnet.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘scales’ ‘tibble’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘memoise’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
Running examples in ‘lime-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_superpixels
> ### Title: Test super pixel segmentation
> ### Aliases: plot_superpixels
> 
> ### ** Examples
> 
> image <- system.file('extdata', 'produce.png', package = 'lime')
> 
> # plot with default settings
> plot_superpixels(image)

 *** caught segfault ***
address 0x108, cause 'memory not mapped'

Traceback:
 1: magick_image_write_frame(image, format = format, i = i)
 2: image_write_frame(image, format = channels)
 3: image_data(x[i])
 4: `[[.magick-image`(image_channel(im_lab, "R"), 1)
 5: image_channel(im_lab, "R")[[1]]
 6: slic(image_channel(im_lab, "R")[[1]][1, , ], image_channel(im_lab,     "G")[[1]][1, , ], image_channel(im_lab, "B")[[1]][1, , ],     n_sp = n_superpixels, weight = weight, n_iter = n_iter)
 7: plot_superpixels(image)
An irrecoverable exception occurred. R is aborting now ...
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.1Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    R          1.3Mb
    doc        2.4Mb
    libs      21.9Mb
    testdata   1.6Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘logistf-Ex.R’ failed
The error most likely occurred in:

> ### Name: pool.RR
> ### Title: Compute Pooled Normal Confidence Intervals (following Rubin's
> ###   Rules) after Multiple Imputation
> ### Aliases: pool.RR
> ### Keywords: regression models
> 
> ### ** Examples
> 
> #generate data set with NAs
> freq=c(5,2,2,7,5,4)
> y<-c(rep(1,freq[1]+freq[2]), rep(0,freq[3]+freq[4]), rep(1,freq[5]), rep(0,freq[6]))
> x<-c(rep(1,freq[1]), rep(0,freq[2]), rep(1,freq[3]), rep(0,freq[4]), rep(NA,freq[5]),
+    rep(NA,freq[6]))
> toy<-data.frame(x=x,y=y)
> 
> 
> # impute data set 5 times
> set.seed(169)
> toymi<-list(0)
> for(i in 1:5){
+   toymi[[i]]<-toy
+   y1<-toymi[[i]]$y==1 & is.na(toymi[[i]]$x)
+   y0<-toymi[[i]]$y==0 & is.na(toymi[[i]]$x)
+   xnew1<-rbinom(sum(y1),1,freq[1]/(freq[1]+freq[2]))
+   xnew0<-rbinom(sum(y0),1,freq[3]/(freq[3]+freq[4]))
+   toymi[[i]]$x[y1==TRUE]<-xnew1
+   toymi[[i]]$x[y0==TRUE]<-xnew0
+ }
> 
> 
> # logistf analyses of each imputed data set
> fit.list<-lapply(1:5, function(X) logistf(data=toymi[[X]], y~x, pl=TRUE, dataout=TRUE))
> summary(pool.RR(fit.list))
Error in sqrt(x$t) : non-numeric argument to mathematical function
Calls: summary -> summary.mipo
Execution halted
Namespaces in Imports field not imported from:
  ‘NLRoot’ ‘ade4’ ‘glmnet’ ‘lars’ ‘lattice’ ‘logmult’ ‘pdist’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘knitr’
  All declared Imports should be used.
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  46.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cmprsk’ ‘colorspace’ ‘etm’ ‘fracdiff’ ‘gtable’ ‘munsell’
  ‘numDeriv’ ‘plyr’ ‘quadprog’ ‘scales’ ‘timeDate’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   5.0Mb
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/ManifoldOptim.Rcheck/00install.out’ for details.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Error in re-building vignettes:
  ...
Package:  markovchain
Version:  0.6.9.10
Date:     2018-06-01
BugReport: http://github.com/spedygiorgio/markovchain/issues


Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: msm
Loading required package: survival
Loading required package: matlab

Attaching package: 'matlab'

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

    reshape

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

    find, fix

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

    sum

Warning in assessOrder(rain$rain) :
  The correctes of this function is in question. It will be deeply revised in the forthcoming versions.
Warning in assessStationarity(rain$rain, 10) :
  The correctes of this function is in question. It will be deeply revised in the forthcoming versions.
Warning in chisq.test(mat) : Chi-squared approximation may be incorrect
Warning in chisq.test(mat) : Chi-squared approximation may be incorrect
Warning in chisq.test(mat) : Chi-squared approximation may be incorrect
Loading required package: ctmcd
Loading required package: expm
Loading required package: Matrix

Attaching package: 'expm'

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

    expm

This function is experimental
Error reading bibliography ./markovchainBiblio.bib (line 468, column 12):
unexpected ","
expecting white space
Error running filter /usr/local/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'GSoC-2017_additions.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
File ‘maxent/libs/maxent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespaces in Imports field not imported from:
  ‘graphics’ ‘mds’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   8.0Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RGtk2’ ‘RNifti’ ‘cairoDevice’ ‘gtools’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘foreign’ ‘formattable’ ‘ggplot2’
  ‘haven’ ‘magrittr’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespace in Imports field not imported from: ‘rattle’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘reshape’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘shiny’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/mets.Rcheck/00install.out’ for details.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  16.2Mb
    misc   1.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘mFilter/R/zzz.R’:
  .onLoad calls:
    writeLines(strwrap(txt, indent = 4, exdent = 4))

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

.onLoad: warning in packageDescription("mFilter", lib = mylib): partial
  argument match of 'lib' to 'lib.loc'
bkfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
cffilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  19.7Mb
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘copula’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘jpeg’
  All declared Imports should be used.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.4Mb
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/missDeaths.Rcheck/00install.out’ for details.
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   4.0Mb
Namespace in Imports field not imported from: ‘rjags’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘deSolve’ ‘progress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘foreach’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘iterators’ ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sparsepp’
  All declared Imports should be used.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   2.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
Namespace in Imports field not imported from: ‘ratelimitr’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.7Mb
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    libs  44.7Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
Running examples in ‘MultiABEL-Ex.R’ failed
The error most likely occurred in:

> ### Name: MultiLoad
> ### Title: Load individual-level data for multivariate GWA analysis
> ### Aliases: MultiLoad MultiLoad, multiload
> ### Keywords: load multiload, multivariate,
> 
> ### ** Examples
> 
> 
> ## loading example gwaa.data in GenABEL
> require(GenABEL)
Loading required package: GenABEL
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GenABEL’
> data(ge03d2ex.clean)
Warning in data(ge03d2ex.clean) : data set ‘ge03d2ex.clean’ not found
> 
> ## running multivariate GWAS for 3 traits: height, weight, bmi
> loaded <- MultiLoad(gwaa.data = ge03d2ex.clean, trait.cols = c(5, 6, 8), 
+                     covariate.cols = c(2, 3))
loading data ...Error in MultiLoad(gwaa.data = ge03d2ex.clean, trait.cols = c(5, 6, 8),  : 
  object 'ge03d2ex.clean' not found
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 75.9Mb
  sub-directories of 1Mb or more:
    libs  75.7Mb
Namespaces in Imports field not imported from:
  ‘boot’ ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘survival’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R     2.3Mb
    doc   4.4Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘knitr’
  All declared Imports should be used.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
Namespace in Imports field not imported from: ‘biomartr’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
Running examples in ‘NAM-Ex.R’ failed
The error most likely occurred in:

> ### Name: GWP
> ### Title: Genome-wide prediction
> ### Aliases: wgr ben
> 
> ### ** Examples
> 
> # Load data
> data(tpod)
> 
> # BLUP
> BRR = wgr(y,gen,iv=FALSE,pi=0,it=200,bi=50)
> cor(y,BRR$hat)
          [,1]
[1,] 0.6981897
> 
> # BayesA
> BayesA = wgr(y,gen,iv=TRUE,pi=0,it=200,bi=50)
> cor(y,BayesA$hat)
          [,1]
[1,] 0.6919416
> 
> # BayesB
> BayesB = wgr(y,gen,iv=TRUE,pi=.95,it=200,bi=50)
> cor(y,BayesB$hat)
          [,1]
[1,] 0.5915633
> 
> # BayesC
> BayesC = wgr(y,gen,iv=FALSE,pi=.95,it=200,bi=50)
> cor(y,BayesC$hat)
         [,1]
[1,] 0.476323
> 
> # BayesL
> BayesL = wgr(y,gen,de=TRUE,it=200,bi=50)
> cor(y,BayesL$hat)
          [,1]
[1,] 0.6656239
> 
> # Bagging  BLUP
> Bag = wgr(y,gen,bag=0.999,it=200,bi=50)
Error in crossprod(x, y) : 
  requires numeric/complex matrix/vector arguments
Calls: wgr -> crossprod
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   6.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘lme4’ ‘stringi’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Namespaces in Imports field not imported from:
  ‘ProjectTemplate’ ‘devtools’ ‘plyr’ ‘survival’
  All declared Imports should be used.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              5.5Mb
    classic-bugs   1.6Mb
    include        5.8Mb
    tests          1.3Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Namespace in Imports field not imported from: ‘deSolve’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘geosphere’ ‘lwgeom’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’
  ‘forcats’ ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/npcp.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  14.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Note: found 13172 marked Latin-1 strings
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OECD)
  > 
  > test_check("OECD")
  <XMLInputError: XML content does not seem to be XML: ''>
  ── 1. Error: get_data_structure returns a list of data frame with positive lengt
  trying to get slot "concepts" from an object of a basic class ("NULL") with no slots
  1: get_data_structure(dataset) at testthat/tests.R:4
  2: data.frame(data_structure@concepts)
  
  <XMLInputError: XML content does not seem to be XML: ''>
  ── 2. Failure: get_dataset returns a data frame with positive length (@tests.R#1
  nrow(df) > 0 isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 2
  1. Error: get_data_structure returns a list of data frame with positive length (@tests.R#4) 
  2. Failure: get_dataset returns a data frame with positive length (@tests.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 68-70 (oecd_vignette_main.Rmd) 
Error: processing vignette 'oecd_vignette_main.Rmd' failed with diagnostics:
trying to get slot "concepts" from an object of a basic class ("NULL") with no slots
Execution halted
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is 97.8Mb
  sub-directories of 1Mb or more:
    libs  97.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
installed size is 147.8Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    libs    137.9Mb
    models    4.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.2Mb
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/osc.Rcheck/00install.out’ for details.
Running examples in ‘osi-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Peer's Certificate has expired.
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Package suggested but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.1Mb
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW: warning in return(x@u1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@u2): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@w1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW: warning in x@u1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@u2 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@w1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   9.5Mb
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    lib   9.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   6.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
Found the following significant warnings:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/Peaks.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘cluster’ ‘graph’
  All declared Imports should be used.
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/PhaseType.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘DT’ ‘leaflet’ ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
Found the following significant warnings:
  phreeqcpp/cvode.cpp:3783:8: warning: explicitly assigning value of variable of type 'realtype' (aka 'double') to itself [-Wself-assign]
  phreeqcpp/model.cpp:3047:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/model.cpp:3048:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:142:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:155:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:167:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:179:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:193:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:205:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/transport.cpp:630:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/phreeqc.Rcheck/00install.out’ for details.
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.3Mb
Namespaces in Imports field not imported from:
  ‘gplots’ ‘phytools’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘lubridate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘covr’ ‘knitr’
  All declared Imports should be used.
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘RColorBrewer’ ‘arm’ ‘epiDisplay’ ‘foreign’ ‘gbm’
  ‘grid’ ‘lattice’ ‘latticeExtra’ ‘lme4’ ‘nnet’ ‘parallel’ ‘splines’
  ‘survey’ ‘twang’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.0Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘PKNCA’ ‘grid’ ‘magrittr’ ‘plyr’ ‘xpose’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Found the following significant warnings:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/powell.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ppcctest_pearson3.c:19:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/ppcc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./shared.h:67:9: warning: result of comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/praznik.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.6Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
Namespaces in Imports field not imported from:
  ‘DiagrammeRsvg’ ‘RColorBrewer’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘clipr’ ‘desc’ ‘devtools’
  All declared Imports should be used.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      5.6Mb
Package suggested but not available for checking: ‘qtbase’
Namespace in Imports field not imported from: ‘distcrete’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Files which contain pragma(s) suppressing diagnostics:
  ‘src/geobuf.pb.h’ ‘src/rexp.pb.h’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbkrtest’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   2.4Mb
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ptinpoly.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.3Mb
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘descr’ ‘gee’ ‘lme4’ ‘nlme’ ‘nnet’ ‘ordinal’ ‘pander’
  ‘papeR’ ‘rmdformats’ ‘visreg’
  All declared Imports should be used.
installed size is 39.9Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Compilation used the following non-portable flag(s):
  ‘-Werror=format-security’ ‘-Wp,-D_FORTIFY_SOURCE=2’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/QPot.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       2.9Mb
    libs      1.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  12.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.9Mb
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘writexl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘psych’ ‘rstudioapi’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   9.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dtplyr’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
Running examples in ‘raptr-Ex.R’ failed
The error most likely occurred in:

> ### Name: make.DemandPoints
> ### Title: Generate demand points for RAP
> ### Aliases: make.DemandPoints
> 
> ### ** Examples
> 
> # load data
> data(cs_spp, cs_space)
> 
> # generate species points
> species.points <- randomPoints(cs_spp[[1]], n = 100, prob = TRUE)
> env.points <- raster::extract(cs_space, species.points)
> 
> # generate demand points for a 1d space using ks
> dps1 <- make.DemandPoints(points = env.points[,1], kernel.method = "ks")
> 
> # generate demand points for a 2d space using hypervolume
> dps2 <- make.DemandPoints(points = env.points,
+                           kernel.method = "hypervolume",
+                           samples.per.point = 10)

Building tree... 
done.
Ball query... 

done.
Error in pb_update(self, private, ratio, tokens) : 
  !self$finished is not TRUE
Calls: make.DemandPoints ... hypervolume_threshold -> <Anonymous> -> pb_update -> stopifnot
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.1Mb
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Namespace in Imports field not imported from: ‘lme4’
  All declared Imports should be used.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   7.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Package suggested but not available for checking: ‘ROpenOffice’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
    libs      1.4Mb
Error in re-building vignettes:
  ...
! LaTeX Error: Lonely \item--perhaps a missing list environment.

Error: processing vignette 'RcppArmadillo-sparseMatrix.Rmd' failed with diagnostics:
Failed to compile RcppArmadillo-sparseMatrix.tex. See RcppArmadillo-sparseMatrix.log for more info.
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Found the following warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/data/gannet/ripley/R/packages/tests-clang/RcppBlaze.Rcheck/00install.out’ for details.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    include  25.5Mb
    libs      1.8Mb
Error in re-building vignettes:
  ...
running: python  -c 'import numpy as np

mat = np.arange(12).reshape(3,4) * 1.1
np.save("fmat.npy", mat)
print mat

vec = np.arange(5) * 1.1
np.save("fvec.npy", vec)
print vec'
running: python  -c 'import numpy as np  
m = np.load("randmat.npy")
print m
v = np.load("simplevec.npy")
print v'
! LaTeX Error: Lonely \item--perhaps a missing list environment.

Error: processing vignette 'RcppCNPy-intro.Rmd' failed with diagnostics:
Failed to compile RcppCNPy-intro.tex. See RcppCNPy-intro.log for more info.
Execution halted
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     23.5Mb
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      39.2Mb
    libs     11.3Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.6Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     14.0Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.4Mb
    libs      4.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘smcure’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rcompression’
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/rdist.Rcheck/00install.out’ for details.
Subdirectory ‘src’ contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   8.6Mb
Namespaces in Imports field not imported from:
  ‘sjmisc’ ‘stringr’
  All declared Imports should be used.
Found the following apparent object files/libraries:
  inst/obj/cube.obj inst/obj/cube_badmtl.obj
Object files/libraries should not be included in a source package.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   4.5Mb
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  16.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘nnet’ ‘purrr’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘Rcplex’
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
Namespaces in Imports field not imported from:
  ‘compiler’ ‘data.table’
  All declared Imports should be used.
Found the following significant warnings:
  gar.c:356:29: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  gar.c:356:80: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/repeated.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.8Mb
Namespace in Imports field not imported from: ‘gdalUtils’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘methods’
  All declared Imports should be used.
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    libs  50.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.6Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.6Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
Rjava.init.warning: stack size reduced from unlimited to 7957504 bytes after JVM initialization.
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.5Mb
    libs   8.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc   9.8Mb
Found the following significant warnings:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RHRV.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘gWidgetsRGtk2’
  All declared Imports should be used.
Found the following significant warnings:
  computePvals.c:488:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ridge.Rcheck/00install.out’ for details.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONGlobals.h:44:49: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONSharedString.h:180:47: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:182:66: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  JSONValidator.cpp:394:105: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  JSONValidator.cpp:397:104: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  JSONStream.cpp:8:130: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:8:157: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONStream.cpp:12:64: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:12:100: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  internalJSONNode.cpp:78:117: warning: field '_name_encoded' will be initialized after field '_name' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/RJSONIO.Rcheck/00install.out’ for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    exe  23.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘knitr’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    rmd   6.9Mb
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of 'full' to 'full.names'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: no visible global function definition for ‘quantile’
diagnos.envel: no visible global function definition for ‘qnorm’
diagnos.envel: no visible binding for global variable ‘quantile’
hrplot: no visible global function definition for ‘plot’
hrplot: no visible global function definition for ‘lines’
hrplot: no visible global function definition for ‘abline’
hrplot: no visible global function definition for ‘text’
sim.chain: no visible global function definition for ‘rnorm’
simRandWalk: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline lines plot qnorm quantile rnorm text
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
File ‘RMC/libs/RMC.so’:
  Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’
File ‘RMC/libs/RMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.4Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rmweather)
  > 
  > test_check("rmweather")
  ── 1. Failure: Test training function (@test_02_rmw_functions.R#53)  ───────────
  model$r.squared not equal to 0.4184627.
  1/1 mismatches
  [1] 0.399 - 0.418 == -0.0196
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 32 SKIPPED: 0 FAILED: 1
  1. Failure: Test training function (@test_02_rmw_functions.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
installed size is 97.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     95.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R   9.7Mb
Found the following significant warnings:
  ./hammock.h:369:15: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/robfilter.Rcheck/00install.out’ for details.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for ‘prediction’
o.rocc: no visible global function definition for ‘performance’
o.rocc: no visible global function definition for ‘binom.test’
tr.rocc: no visible global function definition for ‘prediction’
tr.rocc: no visible global function definition for ‘performance’
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
Warning: parse error in file 'testthat/Rd-example-5.R':
1:1: unexpected input
1: \
    ^
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.5Mb
Running examples in ‘rphylotastic-Ex.R’ failed
The error most likely occurred in:

> ### Name: taxa_get_taxonomic_tree
> ### Title: Get taxonomic tree from the NCBI
> ### Aliases: taxa_get_taxonomic_tree
> 
> ### ** Examples
> 
> taxa <- c("Setophaga striata", "Setophaga magnolia",
+      "Setophaga angelae", "Setophaga plumbea",
+      "Setophaga virens")
> phy <- taxa_get_taxonomic_tree(taxa)
Error in open.connection(con, "rb") : HTTP error 500.
Calls: taxa_get_taxonomic_tree ... fromJSON_string -> parseJSON -> parse_con -> open -> open.connection
Execution halted
Running ‘test-all.R’ [4s/30s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ###
  > library(testthat)
  > test_check('rphylotastic')
  Loading required package: rphylotastic
  ── 1. Error: Loading a tree from NCBI taxonomy (@test_tree.R#17)  ──────────────
  HTTP error 500.
  1: taxa_get_taxonomic_tree(taxa) at testthat/test_tree.R:17
  2: jsonlite::fromJSON(paste(get_base_url(), "gt/pt/get_tree?taxa=", taxa.string, sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 36 SKIPPED: 0 FAILED: 1
  1. Error: Loading a tree from NCBI taxonomy (@test_tree.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.2Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.3Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.3Mb
Namespace in Imports field not imported from: ‘vegan’
  All declared Imports should be used.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘tcltk’ ‘tools’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 52.5Mb
  sub-directories of 1Mb or more:
    libs  51.9Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Namespace in Imports field not imported from: ‘pkgconfig’
  All declared Imports should be used.
Found the following significant warnings:
  :481:10: warning: 'long long' is a C++11 extension [-Wc++11-long-long]    #pragma clang diagnostic pop
  : warning: 'long long' is a C++11 extension [-Wc++11-long-long]1307535010540395uLL
  :477:10: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/rstanarm.Rcheck/00install.out’ for details.
installed size is 157.4Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    doc     2.9Mb
    libs  152.5Mb
installed size is 293.7Mb
  sub-directories of 1Mb or more:
    libs  291.1Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    Lib  11.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.5Mb
    projects   2.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Namespace in Imports field not imported from: ‘TTR’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.0Mb
Namespace in Imports field not imported from: ‘RGtk2’
  All declared Imports should be used.
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  41.5Mb
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
    test  19.6Mb
Error in re-building vignettes:
  ...
Quitting from lines 293-299 (vignette.Rnw) 
Error: processing vignette 'vignette.Rnw' failed with diagnostics:
there is no package called 'GenABEL'
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/RWiener.Rcheck/00install.out’ for details.
Found the following significant warnings:
  nchg.c:555:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RxCEcolInf.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Found the following significant warnings:
  yacas/src/obmalloc.cpp:584:23: warning: result of comparison of constant 384307168202282325 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Ryacas.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs    7.5Mb
    yacas   1.5Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘subplex’
  All declared Imports should be used.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SafeBayes.Rcheck/00install.out’ for details.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Namespaces in Imports field not imported from:
  ‘purrr’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘testthat’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    2.4Mb
    libs   2.1Mb
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SDMTools.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘BayesX’ ‘rsvd’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.1Mb
    doc    1.2Mb
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/Segmentor3IsBack.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
plot.SEL: no visible global function definition for ‘plot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘purrr’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘XML’ ‘mgcv’
  All declared Imports should be used.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs  12.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Found the following significant warnings:
  vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    doc     10.8Mb
    libs     6.1Mb
    sqlite   1.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.3Mb
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘htmlwidgets’ ‘jsonlite’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘gridExtra’ ‘knitr’ ‘latticeExtra’ ‘msm’ ‘plotly’
  ‘shinyBS’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    www   6.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  10.9Mb
File ‘simpleboot/R/zzz.R’:
  .onLoad calls:
    require(boot)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

lo.boot.resample: warning in sample(1:nrow(orig.data), rep = TRUE, prob
  = weights): partial argument match of 'rep' to 'replace'
lo.boot.resample: warning in sample(res, rep = TRUE, prob = weights):
  partial argument match of 'rep' to 'replace'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.9Mb
Namespaces in Imports field not imported from:
  ‘BB’ ‘MASS’ ‘ggplot2’ ‘grid’ ‘triangle’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.8Mb
Namespace in Imports field not imported from: ‘mcmc’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.0Mb
installed size is 43.1Mb
  sub-directories of 1Mb or more:
    libs  41.8Mb
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SMCP.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.4Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘nlme’ ‘survival’
  All declared Imports should be used.
Found the following significant warnings:
  /usr/include/python2.7/unicodeobject.h:534:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:553:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:575:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:593:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:173:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:174:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:175:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/data/gannet/ripley/R/packages/tests-clang/SnakeCharmR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./snappy-stubs-internal.h:95:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/snappier.Rcheck/00install.out’ for details.
Running examples in ‘SNPtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: categorize.variants
> ### Title: categorize.variants
> ### Aliases: categorize.variants
> 
> ### ** Examples
> 
>   data(example.snps)
>   snp.type = categorize.variants(variants = example.snps[1:50,])
Error in open.TabixFile(con) : 
  [khttp_connect_file] fail to open file (HTTP code: 404).
Calls: categorize.variants -> get.mgi.features -> open -> open.TabixFile
Execution halted
Error in re-building vignettes:
  ...
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    expand.grid

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

    strsplit

Loading required package: Rsamtools

Error: processing vignette 'SNPtools.Rnw' failed with diagnostics:
 chunk 3 
Error in open.TabixFile(con) : 
  [khttp_connect_file] fail to open file (HTTP code: 404).

Execution halted
Namespaces in Imports field not imported from:
  ‘gtools’ ‘hashmap’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
'::' or ':::' import not declared from: ‘microbenchmark’
'library' or 'require' call not declared from: ‘magrittr’
Running ‘test-all.R’ [119s/121s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  ── 1. Failure: simList object initializes correctly (@test-simList.R#17)  ──────────────────────────
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 36.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  34.4Mb
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.8Mb
    help   5.0Mb
    libs   1.9Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
Found the following significant warnings:
  Warning: namespace ‘Biobase’ is not available and has been replaced
  Warning: namespace ‘bigmemory’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-clang/spectralAnalysis.Rcheck/00install.out’ for details.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Error in re-building vignettes:
  ...
## ----- This is spikeSlabGAM 1.1-11 ----- ##
Please note that a recent update to gridExtra has made it necessary
  to change the interface for <plot.spikeSlabGAM> starting in version 1.1-9.
Instead of arguments 'rows', 'cols', 'widths', 'heights', 'maxPlotsPerPage',
  it now accepts only 'nrow' and 'ncol'.
Arguments 'widths' & 'heights' can still be defined and are handed over
  to <gridExtra:::marrangeGrob>.
Sorry for the inconvenience.
Loading required package: parallel
Loading required package: stabs
This is mboost 2.9-0. See 'package?mboost' and 'news(package  = "mboost")'
for a complete list of changes.


Attaching package: 'ggplot2'

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

    %+%

Warning in (function (xnew)  :
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots,  :
  Some 'x' values are beyond 'boundary.knots'; Linear extrapolation used.
Warning in (function (xnew)  :
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingSpikeSlabGAM.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘splitstackshape-Ex.R’ failed
The error most likely occurred in:

> ### Name: cSplit_f
> ### Title: Split Concatenated Cells in a data.frame or a data.table
> ### Aliases: cSplit_f
> 
> ### ** Examples
> 
> 
> ## Sample data. Change `n` to larger values to test on larger data
> set.seed(1)
> n <- 10
> mydf <- data.frame(id = sequence(n))
> mydf <- within(mydf, {
+   v3 <- do.call(paste, c(data.frame(matrix(sample(
+   letters, n*4, TRUE), ncol = 4)), sep = "_"))
+   v2 <- do.call(paste, c(data.frame(matrix(sample(
+   LETTERS, n*3, TRUE), ncol = 3)), sep = "."))
+   v1 <- do.call(paste, c(data.frame(matrix(sample(
+   10, n*2, TRUE), ncol = 2)), sep = "-"))
+ })
> mydf
   id   v1    v2      v3
1   1  4-5 V.M.X g_f_y_m
2   2  9-8 Q.W.H j_e_f_p
3   3  4-4 U.L.L o_r_q_m
4   4  4-4 O.G.I x_j_d_e
5   5  5-8 N.B.Q f_u_g_v
6   6  9-3 U.C.G x_m_k_r
7   7  9-8 A.I.M y_s_a_u
8   8  4-2 M.N.T r_z_j_c
9   9  8-3 T.R.C q_j_w_s
10 10 10-2 S.K.W b_u_i_k
> 
> cSplit_f(mydf, splitCols = c("v1", "v2", "v3"), sep = c("-", ".", "_"))
Error in fread(x, sep[i], header = FALSE) : 
  You can provide 'input=' or 'file=', not both.
Calls: cSplit_f -> fread
Execution halted
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   7.7Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  12.0Mb
Namespaces in Imports field not imported from:
  ‘BayesX’ ‘BayesXsrc’ ‘automap’ ‘plyr’ ‘rgdal’ ‘splines’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stabledist’
  All declared Imports should be used.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   9.1Mb
    lib       1.5Mb
Namespaces in Imports field not imported from:
  ‘readr’ ‘tools’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘statnet’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘statnet’
See ‘/data/gannet/ripley/R/packages/tests-clang/statnet.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘VennDiagram’ ‘lattice’ ‘openair’ ‘rlist’ ‘tm’ ‘wordcloud’ ‘zoo’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespace in Imports field not imported from: ‘knitcitations’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Found the following significant warnings:
  BIRCH/CFTree.cpp:18:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/stream.Rcheck/00install.out’ for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   9.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
Running ‘testthat.R’ [8s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  ── 1. Error: child process is terminated in Linux (@test-termination.R#85)  ────
  is_process_handle(handle) is not TRUE
  1: expect_true(wait_until_appears(child_id)) at testthat/test-termination.R:85
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: wait_until_appears(child_id)
  5: process_wait(handle, TIMEOUT_IMMEDIATE) at /data/gannet/ripley/R/packages/tests-clang/subprocess.Rcheck/tests/testthat/helper-processes.R:58
  6: stopifnot(is_process_handle(handle))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 71 SKIPPED: 2 FAILED: 1
  1. Error: child process is terminated in Linux (@test-termination.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘classInt’ ‘grDevices’ ‘graphics’ ‘pixmap’ ‘rgeos’
  ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SuppDists.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘matrixStats’ ‘nloptr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.5Mb
installed size is 69.6Mb
  sub-directories of 1Mb or more:
    libs  68.7Mb
Namespace in Imports field not imported from: ‘cowplot’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/svd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/SWATmodel.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    sql   8.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    apps   2.8Mb
    libs   8.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Namespaces in Imports field not imported from:
  ‘nlme’ ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘tergm’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘tergm’
See ‘/data/gannet/ripley/R/packages/tests-clang/tergm.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   5.3Mb
Namespace in Imports field not imported from: ‘irlba’
  All declared Imports should be used.
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    3.8Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘splancs’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dbplyr’ ‘reprex’ ‘rlang’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/TimeMachine.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘forecast’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    rmarkdown   1.3Mb
Namespaces in Imports field not imported from:
  ‘rvest’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘tibble’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.3Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    examples  14.9Mb
    include    3.0Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
Note: found 42 marked Latin-1 strings
  Note: found 360 marked UTF-8 strings
File ‘tpr/libs/tpr.so’:
  Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.7Mb
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘nlme’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
Error in re-building vignettes:
  ...
Error reading bibliography ./TropFishR.bib (line 453, column 7):
unexpected ","
expecting white space
Error running filter /usr/local/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'Using_TropFishR_ELEFAN_functions.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespace in Imports field not imported from: ‘gsDesign’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘forecast’
  All declared Imports should be used.
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.
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs       22.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.6Mb
    libs   2.6Mb
Namespace in Imports field not imported from: ‘mcmcplots’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of 'arg' to
  'args'
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.2Mb
    help   2.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tidyr’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc           5.6Mb
    htmlwidgets   4.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    extdata  10.8Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘purrr’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘XML’ ‘checkmate’ ‘gstat’ ‘intervals’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  50.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘XML’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘spThin’ ‘spocc’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘minqa’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
! LaTeX Error: Missing \begin{document}.

Error: processing vignette 'WeightedMixedModels.Rmd' failed with diagnostics:
Failed to compile WeightedMixedModels.tex. See WeightedMixedModels.log for more info.
Execution halted
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/WhopGenome.Rcheck/00install.out’ for details.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Namespaces in Imports field not imported from:
  ‘drc’ ‘imputeTestbench’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RandomFields’ ‘data.table’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Running examples in ‘wtss-Ex.R’ failed
The error most likely occurred in:

> ### Name: WTSS
> ### Title: The WTSS class
> ### Aliases: WTSS WTSS-class WTSS
> 
> ### ** Examples
> 
> ts.server = WTSS("http://www.dpi.inpe.br/tws/wtss")
Error in .parseJSON(.sendRequest(request)) : 
  <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>503 Service Temporarily Unavailable</title>
</head><body>
<h1>Service Temporarily Unavailable</h1>
<p>The server is temporarily unable to service your
request due to maintenance downtime or capacity
problems. Please try again later.</p>
</body></html>
Calls: WTSS ... initialize -> .local -> .listCoverages -> .parseJSON
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
Found the following significant warnings:

  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
  Warning: 'term.list.formula' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘MatchIt’ ‘WhatIf’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/data/gannet/ripley/R/packages/tests-devel/audio.Rcheck/00install.out’ for details.
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘blkergm’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘blkergm’
See ‘/data/gannet/ripley/R/packages/tests-devel/blkergm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘btergm’
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘btergm’
See ‘/data/gannet/ripley/R/packages/tests-devel/btergm.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 55-69 (CDECRetrieve.Rmd) 
Error: processing vignette 'CDECRetrieve.Rmd' failed with diagnostics:
Timeout was reached: Connection timed out after 10001 milliseconds
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.count’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.count’
See ‘/data/gannet/ripley/R/packages/tests-devel/ergm.count.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘ergm::colMeans.mcmc.list’ by ‘statnet.common::colMeans.mcmc.list’ when loading ‘ergm.ego’
  Warning: replacing previous import ‘ergm::sweep.mcmc.list’ by ‘statnet.common::sweep.mcmc.list’ when loading ‘ergm.ego’
See ‘/data/gannet/ripley/R/packages/tests-devel/ergm.ego.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.graphlets’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.graphlets’
See ‘/data/gannet/ripley/R/packages/tests-devel/ergm.graphlets.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.rank’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.rank’
See ‘/data/gannet/ripley/R/packages/tests-devel/ergm.rank.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.userterms’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.userterms’
See ‘/data/gannet/ripley/R/packages/tests-devel/ergm.userterms.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [7s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ess)
  > 
  > test_check("ess")
  ── 1. Failure: show_country_rounds returns correct rounds for countries (@test-s
  show_country_rounds("Italy") not equal to c(1, 2, 6).
  Lengths differ: 4 is not 3
  
  ── 2. Failure: show_country_rounds returns correct rounds for countries (@test-s
  show_country_rounds("Spain") not equal to 1:7.
  Lengths differ: 8 is not 7
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 36 SKIPPED: 23 FAILED: 2
  1. Failure: show_country_rounds returns correct rounds for countries (@test-show_.R#100) 
  2. Failure: show_country_rounds returns correct rounds for countries (@test-show_.R#101) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-devel/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/freetypeharfbuzz.Rcheck/00install.out’ for details.
.ldots.set: no visible global function definition for ‘getS3method’
grf: no visible global function definition for ‘chull’
image.grf: no visible global function definition for ‘heat.colors’
image.krige.bayes: no visible global function definition for
  ‘heat.colors’
legend.krige: no visible global function definition for ‘heat.colors’
points.geodata: no visible global function definition for
  ‘terrain.colors’
points.geodata: no visible global function definition for ‘gray’
read.geodata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  chull getS3method gray heat.colors read.table terrain.colors
Consider adding
  importFrom("grDevices", "chull", "gray", "heat.colors",
             "terrain.colors")
  importFrom("utils", "getS3method", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  _t_array_properties.cpp:10:13: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/gRbase.Rcheck/00install.out’ for details.
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Running examples in ‘imfr-Ex.R’ failed
The error most likely occurred in:

> ### Name: imf_codes
> ### Title: Retrieve individual database codes
> ### Aliases: imf_codes
> 
> ### ** Examples
> 
> # Retrieve indicators from BOP database
> test = imf_codes(codelist = 'CL_INDICATOR_BOP')

Downloading: 3.8 kB     
Downloading: 3.8 kB     
Downloading: 3.8 kB     
Downloading: 3.8 kB     
Downloading: 3.8 kB     
Downloading: 3.8 kB     
Downloading: 11 kB     
Downloading: 11 kB     
Downloading: 25 kB     
Downloading: 25 kB     
Downloading: 38 kB     
Downloading: 38 kB     
Downloading: 47 kB     
Downloading: 47 kB     
Downloading: 64 kB     
Downloading: 64 kB     
Downloading: 80 kB     
Downloading: 80 kB     
Downloading: 91 kB     
Downloading: 91 kB     
Downloading: 93 kB     
Downloading: 93 kB     
Downloading: 100 kB     
Downloading: 100 kB     
Downloading: 120 kB     
Downloading: 120 kB     
Downloading: 130 kB     
Downloading: 130 kB     
Downloading: 150 kB     
Downloading: 150 kB     
Downloading: 150 kB     
Downloading: 150 kB     
Downloading: 150 kB     
Downloading: 150 kB     
Downloading: 150 kB     
Downloading: 150 kB     Error: Unable to download series.
Execution halted
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import ‘ergm::colMeans.mcmc.list’ by ‘statnet.common::colMeans.mcmc.list’ when loading ‘latentnet’
  Warning: replacing previous import ‘ergm::sweep.mcmc.list’ by ‘statnet.common::sweep.mcmc.list’ when loading ‘latentnet’
See ‘/data/gannet/ripley/R/packages/tests-devel/latentnet.Rcheck/00install.out’ for details.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy
Found the following significant warnings:
  confusionMatrix_.cpp:10:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:12:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:14:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:16:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:57:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:104:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:106:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:108:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:110:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/ModelMetrics.Rcheck/00install.out’ for details.
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...

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 150-156 (utilizando-fetch-proposicao.Rmd) 
Error: processing vignette 'utilizando-fetch-proposicao.Rmd' failed with diagnostics:
API did not return json
Execution halted
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
Found the following significant warnings:
  atkClasses.c:1050:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1058:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1397:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1948:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1964:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8665:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11110:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-devel/RGtk2.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  regTree.c:242:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/RRF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
Found the following significant warnings:
  bitmap.c:1594:29: warning: suggest parentheses around comparison in operand of ‘^’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rttf2pt1.Rcheck/00install.out’ for details.
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Running ‘test-all.R’ [102s/103s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  ── 1. Failure: simList object initializes correctly (@test-simList.R#17)  ──────────────────────────
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: namespace ‘Biobase’ is not available and has been replaced
  Warning: namespace ‘bigmemory’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/spectralAnalysis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  wdl.cpp:184:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/spp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘statnet’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘statnet’
See ‘/data/gannet/ripley/R/packages/tests-devel/statnet.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [8s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stellaRbase)
  > 
  > options(scipen = 25)
  > 
  > test_check("stellaRbase")
  ── 1. Failure: Row counts are correct. (@test-getEffects_Account.R#33)  ────────
  t2[["_embedded"]][["records"]] has length 3, not length 2.
  
  ── 2. Failure: Row counts are correct and consolidate between lists and data tab
  nrow(t8) not equal to 2.
  1/1 mismatches
  [1] 3 - 2 == 1
  
  ── 3. Failure: Row counts are as expected. (@test-getPayments_Account.R#30)  ───
  t2[["_embedded"]][["records"]] has length 2, not length 1.
  
  ── 4. Failure: Row counts consolidate between lists and data tables. (@test-getP
  nrow(t6) not equal to 1.
  1/1 mismatches
  [1] 2 - 1 == 1
  
  ── 5. Failure: Row counts are as expected. (@test-getTransactions_Account.R#31) 
  t2[["_embedded"]][["records"]] has length 2, not length 1.
  
  ── 6. Failure: Row counts consolidate between lists and data tables. (@test-getT
  nrow(t7) not equal to 1.
  1/1 mismatches
  [1] 2 - 1 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 208 SKIPPED: 0 FAILED: 6
  1. Failure: Row counts are correct. (@test-getEffects_Account.R#33) 
  2. Failure: Row counts are correct and consolidate between lists and data tables. (@test-getEffects_Account.R#52) 
  3. Failure: Row counts are as expected. (@test-getPayments_Account.R#30) 
  4. Failure: Row counts consolidate between lists and data tables. (@test-getPayments_Account.R#39) 
  5. Failure: Row counts are as expected. (@test-getTransactions_Account.R#31) 
  6. Failure: Row counts consolidate between lists and data tables. (@test-getTransactions_Account.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [8s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  ── 1. Error: child process is terminated in Linux (@test-termination.R#85)  ────
  is_process_handle(handle) is not TRUE
  1: expect_true(wait_until_appears(child_id)) at testthat/test-termination.R:85
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: wait_until_appears(child_id)
  5: process_wait(handle, TIMEOUT_IMMEDIATE) at /data/gannet/ripley/R/packages/tests-devel/subprocess.Rcheck/tests/testthat/helper-processes.R:58
  6: stopifnot(is_process_handle(handle))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 71 SKIPPED: 2 FAILED: 1
  1. Error: child process is terminated in Linux (@test-termination.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/SWATmodel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘tergm’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘tergm’
See ‘/data/gannet/ripley/R/packages/tests-devel/tergm.Rcheck/00install.out’ for details.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Rglpk' 'corrplot' 'lattice' 'rgl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
multiplot: no visible global function definition for 'rainbow'
multiplot: no visible global function definition for 'plot'
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 'plot'
plot.abf2: no visible global function definition for 'abline'
plot.abf2: no visible global function definition for 'text'
plot.abf2split: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline lines par plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "plot", "text")
to your NAMESPACE file.
fillCSVData: no visible global function definition for 'read.table'
fillData: no visible global function definition for 'edit'
plotGraphs: no visible global function definition for 'par'
plotGraphs: no visible global function definition for 'plot'
plotGraphs: no visible global function definition for 'lines'
plotGraphs: no visible global function definition for 'legend'
plotGraphs: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new edit legend lines par plot read.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
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.
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.
acm: no visible global function definition for 'read.table'
clusters: no visible global function definition for 'write.matrix'
clusters: no visible global function definition for 'dev.new'
clusters: no visible global function definition for 'par'
clusters: no visible global function definition for 'hist'
clusters: no visible global function definition for 'legend'
clusters: no visible global function definition for 'pdf'
clusters: no visible global function definition for 'dev.off'
erra: no visible global function definition for 'read.table'
erra: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  dev.new dev.off hist legend par pbeta pdf read.table write.matrix
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "hist", "legend", "par")
  importFrom("stats", "pbeta")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Aggregate: no visible global function definition for 'aggregate'
Aggregate: no visible binding for global variable 'tail'
Aggregate: no visible binding for global variable 'var'
cocktailEnsemble: no visible global function definition for 'glm'
cocktailEnsemble: no visible global function definition for 'binomial'
cocktailEnsemble: no visible global function definition for 'step'
cocktailEnsemble: no visible binding for global variable 'na.omit'
imputeMissings : <anonymous>: no visible global function definition for
  'median'
predict.cocktailEnsemble: no visible global function definition for
  'predict'
Undefined global functions or variables:
  aggregate binomial glm median na.omit predict step tail var
Consider adding
  importFrom("stats", "aggregate", "binomial", "glm", "median",
             "na.omit", "predict", "step", "var")
  importFrom("utils", "tail")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'SemiPar' 'nlme'
  Please remove these calls from your code.
asp: no visible global function definition for 'as.formula'
asp: no visible global function definition for 'var'
aspm: no visible binding for global variable 'X.Declan'
aspm: no visible binding for global variable 'Z.Jaida'
aspm: no visible binding for global variable 'group.vec.Handan'
aspm: no visible global function definition for 'as.formula'
aspm: no visible global function definition for 'glm'
aspm: no visible global function definition for 'binomial'
aspm: no visible global function definition for 'poisson'
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'Matrix' 'coda' 'mvtnorm' 'MCMCpack' 'spatstat' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'MCMCpack' 'Matrix' 'coda' 'mvtnorm' 'parallel' 'spatstat'
  Please remove these calls from your code.
Package in Depends field not imported from: 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.7Mb
    pictures   2.1Mb
closure_total_fair: no visible global function definition for 'is'
closure_transitive: no visible global function definition for 'is'
de_transitive: no visible global function definition for 'is'
get_equivalence_classes: no visible global function definition for 'is'
get_incomparable_pairs: no visible global function definition for 'is'
get_independent_sets: no visible global function definition for 'is'
is_reflexive: no visible global function definition for 'is'
is_total: no visible global function definition for 'is'
is_transitive: no visible global function definition for 'is'
pareto2_estimate_mle: no visible global function definition for
  'uniroot'
pareto2_test_f: no visible global function definition for 'qf'
pareto2_test_f: no visible global function definition for 'pf'
plot.citfun: no visible global function definition for 'plot'
plot.citfun: no visible global function definition for 'par'
plot.citfun: no visible global function definition for 'segments'
plot.citfun: no visible global function definition for 'points'
plot_producer: no visible global function definition for 'plot'
plot_producer: no visible global function definition for 'par'
plot_producer: no visible global function definition for 'segments'
plot_producer: no visible global function definition for 'points'
rpareto2: no visible global function definition for 'runif'
Undefined global functions or variables:
  is par pf plot points qf runif segments uniroot
Consider adding
  importFrom("graphics", "par", "plot", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "pf", "qf", "runif", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespace with empty importFrom: 'survival'
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'survival'
A package should be listed in only one of these fields.
backfit.cox.interaction: no visible global function definition for
  'coxph'
backfit.lm.interaction: no visible global function definition for 'lm'
backfit.logistic.interaction: no visible global function definition for
  'glm'
backfit.logistic.main: no visible global function definition for 'glm'
cox.interaction: no visible global function definition for 'coxph'
cv.cox.interaction: no visible global function definition for 'coxph'
cv.cox.main: no visible global function definition for 'coxph'
cv.lm.interaction: no visible global function definition for 'lm'
cv.lm.main: no visible global function definition for 'lm'
cv.logistic.interaction: no visible global function definition for
  'glm'
cv.logistic.main: no visible global function definition for 'glm'
lm.interaction: no visible global function definition for 'lm'
logistic.interaction: no visible global function definition for 'glm'
logistic.main: no visible global function definition for 'glm'
Undefined global functions or variables:
  coxph glm lm
Consider adding
  importFrom("stats", "glm", "lm")
to your NAMESPACE file.
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.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
akmeans: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans
Consider adding
  importFrom("stats", "kmeans")
to your NAMESPACE file.
adpbar: no visible global function definition for 'optim'
alabama: no visible global function definition for 'optim'
auglag: no visible global function definition for 'modifyList'
auglag1: no visible global function definition for 'optim'
auglag1: no visible global function definition for 'nlminb'
auglag2: no visible global function definition for 'optim'
auglag2: no visible global function definition for 'nlminb'
auglag3: no visible global function definition for 'optim'
auglag3: no visible global function definition for 'nlminb'
augpen: no visible global function definition for 'optim'
constrOptim.nl: no visible global function definition for 'modifyList'
Undefined global functions or variables:
  modifyList nlminb optim
Consider adding
  importFrom("stats", "nlminb", "optim")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
eval.blockdesign: no visible global function definition for
  'model.matrix'
eval.design: no visible global function definition for 'model.matrix'
expand.formula: no visible global function definition for 'as.formula'
model.matrix.formula: no visible global function definition for
  'model.matrix.default'
model.matrix.terms: no visible global function definition for
  'model.matrix.default'
optBlock : set.factors: no visible global function definition for 'C'
optBlock : remove.nesting: no visible global function definition for
  'as.formula'
optBlock: no visible global function definition for 'formula'
optBlock: no visible global function definition for 'model.matrix'
optFederov: no visible global function definition for 'formula'
optFederov: no visible global function definition for 'model.matrix'
optMonteCarlo : RandomLevels: no visible global function definition for
  'runif'
optMonteCarlo : RandomMixture: no visible global function definition
  for 'rexp'
optMonteCarlo : expand: no visible global function definition for
  'model.matrix'
optMonteCarlo: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  C as.formula formula model.matrix model.matrix.default rexp runif
Consider adding
  importFrom("stats", "C", "as.formula", "formula", "model.matrix",
             "model.matrix.default", "rexp", "runif")
to your NAMESPACE file.
hierarchical: no visible global function definition for 'terms'
hierarchical: no visible global function definition for 'loglin'
hierarchical: no visible global function definition for 'dmultinom'
markov: no visible global function definition for 'download.file'
metropolis: no visible global function definition for 'runif'
mpolyListToMat : <anonymous>: no visible global function definition for
  'runif'
polyOptim: no visible global function definition for 'deriv'
print.hierarchical: no visible binding for global variable 'sd'
spectral : summarize: no visible global function definition for 'sd'
subsets : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  combn deriv dmultinom download.file loglin runif sd terms
Consider adding
  importFrom("stats", "deriv", "dmultinom", "loglin", "runif", "sd",
             "terms")
  importFrom("utils", "combn", "download.file")
to your NAMESPACE file.
gascuel: no visible global function definition for 'optim'
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
allanVarSelect: no visible global function definition for 'read.csv'
fitvbiglm: no visible global function definition for 'read.csv'
fitvbiglm: no visible global function definition for 'update'
getbestchunksize: no visible global function definition for 'read.csv'
getbestchunksize: no visible global function definition for
  'object.size'
predictvbiglm: no visible global function definition for 'read.csv'
predictvbiglm: no visible global function definition for 'predict'
predictvbiglm: no visible global function definition for
  'weighted.mean'
readinbigdata : <anonymous>: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  object.size predict read.csv update weighted.mean
Consider adding
  importFrom("stats", "predict", "update", "weighted.mean")
  importFrom("utils", "object.size", "read.csv")
to your NAMESPACE file.
amCSV.amCluster: no visible global function definition for 'write.csv'
amCSV.amPairwise: no visible global function definition for 'write.csv'
amCSV.amUnique: no visible global function definition for 'write.csv'
amCluster: no visible global function definition for 'hclust'
amCluster: no visible global function definition for 'as.dist'
amHTML.amCluster: no visible global function definition for 'browseURL'
amHTML.amPairwise: no visible global function definition for
  'browseURL'
amHTML.amUnique: no visible global function definition for 'browseURL'
amUniqueProfile: no visible global function definition for 'layout'
amUniqueProfile: no visible global function definition for 'par'
amUniqueProfile: no visible global function definition for
  'plot.default'
amUniqueProfile: no visible global function definition for 'points'
amUniqueProfile: no visible global function definition for 'lines'
amUniqueProfile: no visible global function definition for 'arrows'
amUniqueProfile: no visible global function definition for 'text'
amUniqueProfile: no visible global function definition for 'legend'
Undefined global functions or variables:
  arrows as.dist browseURL hclust layout legend lines par plot.default
  points text write.csv
Consider adding
  importFrom("graphics", "arrows", "layout", "legend", "lines", "par",
             "plot.default", "points", "text")
  importFrom("stats", "as.dist", "hclust")
  importFrom("utils", "browseURL", "write.csv")
to your NAMESPACE file.
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
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.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
amltest: no visible global function definition for 'var'
amltest: no visible global function definition for 'optim'
amltest: no visible global function definition for 'lm'
cleanclust: no visible global function definition for 'cor'
cleanclust: no visible global function definition for 'hclust'
cleanclust: no visible global function definition for 'as.dist'
cleanclust: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cor cutree hclust lm optim var
Consider adding
  importFrom("stats", "as.dist", "cor", "cutree", "hclust", "lm",
             "optim", "var")
to your NAMESPACE file.
AMOEBA : Classi: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
random.init.MLPneuron: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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.
Packages in Depends field not imported from:
  'discretization' 'foreign' 'functional' 'stringr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aode: no visible global function definition for 'Compose'
mdl: no visible global function definition for 'cutPoints'
setVar: no visible global function definition for 'Compose'
Undefined global functions or variables:
  Compose cutPoints
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.
plot,ANFIS: no visible binding for global variable 'X'
plotMF,ANFIS : <anonymous>: no visible global function definition for
  'lines'
plotMFs,ANFIS: no visible global function definition for 'par'
Undefined global functions or variables:
  X lines par
Consider adding
  importFrom("graphics", "lines", "par")
to your NAMESPACE file.
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
annot : annotlist: no visible global function definition for
  'read.table'
annot : annotlist: no visible global function definition for
  'write.table'
annot: no visible global function definition for 'flush.console'
annot: no visible global function definition for 'read.table'
annot: no visible global function definition for 'choose.dir'
Undefined global functions or variables:
  choose.dir flush.console read.table write.table
Consider adding
  importFrom("utils", "choose.dir", "flush.console", "read.table",
             "write.table")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'anoint' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
aw_map: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'library' or 'require' call to 'boot' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
varbin: no visible global function definition for 'boot'
Undefined global functions or variables:
  boot
'library' or 'require' call to 'boot' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'boot' 'lme4' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
TSPM: no visible global function definition for 'glm'
TSPM: no visible binding for global variable 'poisson'
TSPM: no visible global function definition for 'hatvalues'
TSPM: no visible global function definition for 'residuals'
TSPM: no visible global function definition for 'deviance'
TSPM: no visible global function definition for 'qchisq'
TSPM: no visible global function definition for 'qf'
TSPM: no visible global function definition for 'pf'
TSPM: no visible global function definition for 'pchisq'
TSPM: no visible global function definition for 'p.adjust'
norm.inttable: no visible global function definition for 'median'
norm.inttable : <anonymous>: no visible global function definition for
  'quantile'
saint_permF: no visible global function definition for 'read.table'
saint_permF: no visible global function definition for 'write.table'
saint_permF: no visible global function definition for 'write.csv2'
tspm_apms: no visible global function definition for 'read.table'
varFilter : <anonymous>: no visible global function definition for
  'median'
varFilter: no visible global function definition for 'median'
varFilter: no visible global function definition for 'quantile'
Undefined global functions or variables:
  deviance glm hatvalues median p.adjust pchisq pf poisson qchisq qf
  quantile read.table residuals write.csv2 write.table
Consider adding
  importFrom("stats", "deviance", "glm", "hatvalues", "median",
             "p.adjust", "pchisq", "pf", "poisson", "qchisq", "qf",
             "quantile", "residuals")
  importFrom("utils", "read.table", "write.csv2", "write.table")
to your NAMESPACE file.
apple: no visible global function definition for 'ginv'
apple: no visible global function definition for 'runif'
deri: no visible global function definition for 'ginv'
logit: no visible global function definition for 'qlogis'
plot.apple: no visible global function definition for 'matplot'
plot.apple: no visible global function definition for 'lines'
y.app: no visible global function definition for 'ginv'
Undefined global functions or variables:
  ginv lines matplot qlogis runif
Consider adding
  importFrom("graphics", "lines", "matplot")
  importFrom("stats", "qlogis", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: 'emulator'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Afun: no visible global function definition for 'corr.matrix'
betahat.app.H: no visible global function definition for 'quad.form'
betahat.app.H: no visible global function definition for
  'quad.form.inv'
cdash.fun: no visible global function definition for 'quad.3form'
cdash.fun: no visible global function definition for 'quad.form'
generate.toy.observations : delta: no visible global function
  definition for 'rmvnorm'
generate.toy.observations : delta: no visible global function
  definition for 'corr.matrix'
object: no visible global function definition for 'quad.form'
opt.1: no visible global function definition for 'optim'
opt.gt.1: no visible global function definition for 'optim'
subsets.fun : select: no visible global function definition for
  'rbinom'
Undefined global functions or variables:
  corr.matrix optim quad.3form quad.form quad.form.inv rbinom rmvnorm
Consider adding
  importFrom("stats", "optim", "rbinom")
to your NAMESPACE file.
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 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.
kristen.colors: no visible global function definition for
  'colorRampPalette'
kristen.colors: no visible global function definition for 'grey'
plot3d.points: no visible global function definition for 'heat.colors'
plot3d.points: no visible global function definition for 'plot'
ragged.image: no visible global function definition for 'heat.colors'
ragged.image: no visible global function definition for 'image'
scatterplot.density: no visible global function definition for 'grey'
scatterplot.density: no visible global function definition for 'image'
scatterplot.density: no visible global function definition for 'abline'
scatterplot.density: no visible global function definition for 'lm'
scatterplot.density: no visible global function definition for 'legend'
vertical.image.legend: no visible global function definition for 'par'
vertical.image.legend: no visible global function definition for
  'image'
vertical.image.legend: no visible global function definition for 'axis'
vertical.image.legend: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box colorRampPalette grey heat.colors image legend lm par
  plot
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
aqDayOfWeekStat: no visible global function definition for 'index'
aqDropHour: no visible global function definition for 'index'
aqFilterOHLCSD: no visible binding for global variable 'sd'
aqHourIndex: no visible global function definition for 'index'
aqHourlyStat: no visible global function definition for 'index'
aqLoadOHLC: no visible global function definition for 'read.csv'
aqLoadSeriesField: no visible global function definition for 'read.csv'
aqLoadXtsFromCsv: no visible global function definition for 'read.csv2'
aqLoadYahooEOD: no visible global function definition for 'read.csv'
aqSaveXtsToCsv: no visible global function definition for 'write.csv2'
aqStoreSeriesField: no visible global function definition for 'index'
aqStoreSeriesField: no visible global function definition for
  'capture.output'
aqStoreSeriesField: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  capture.output index read.csv read.csv2 sd write.csv2 write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "capture.output", "read.csv", "read.csv2",
             "write.csv2", "write.table")
to your NAMESPACE file.
AR1seg_func: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'TSP'
  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.
arfimaOLS: no visible global function definition for 'lm'
arfimaPrep: no visible global function definition for 'aggregate'
arfimaPrep: no visible global function definition for 'arima'
arfimaPrep: no visible global function definition for 'lm'
arfimaPrep: no visible global function definition for 'residuals'
Undefined global functions or variables:
  aggregate arima lm residuals
Consider adding
  importFrom("stats", "aggregate", "arima", "lm", "residuals")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
Packages suggested but not available for checking:
  'sfit' 'expectile' 'HaarSeg' 'mpcbs'
binarize.array: no visible binding for global variable 'sd'
mskmeans: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans sd
Consider adding
  importFrom("stats", "kmeans", "sd")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Package suggested but not available for checking: 'cacheSweave'
Warning: no function found corresponding to methods exports from 'ascii' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' calls in package code:
  'cacheSweave' 'weaver'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'utils:::RtangleSetup'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'survival:::survmean' 'utils:::.SweaveValidFilenameRegexp'
  'utils:::RtangleFinish' 'utils:::RtangleRuncode'
  'utils:::SweaveParseOptions'
  See the note in ?`:::` about the use of this operator.
Unavailable namespace imported from by a ':::' call: 'cacheSweave'
  See the note in ?`:::` about the use of this operator.
S3 methods shown with full name in documentation object 'cbind.ascii':
  'cbind.ascii'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages suggested but not available for checking: 'REBayes' 'Rmosek'
'library' or 'require' calls to packages already attached by Depends:
  'Hmisc' 'splancs'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Hmisc' 'shapefiles' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ASP.Score: no visible global function definition for 'pnorm'
Graphs.Bayesian: no visible global function definition for 'dev.new'
colorhex: no visible global function definition for 'gray'
colorhex: no visible global function definition for 'rgb'
Undefined global functions or variables:
  dev.new gray pnorm rgb
Consider adding
  importFrom("grDevices", "dev.new", "gray", "rgb")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'asreml'
':::' call which should be '::': 'assertive.base:::print_and_capture'
  See the note in ?`:::` about the use of this operator.
Running examples in 'assist-Ex.R' failed
The error most likely occurred in:

> ### Name: anova.ssr
> ### Title: Testing a Non-parametric Function Fitted via Smoothing Splines
> ### Aliases: anova.ssr
> ### Keywords: file
> 
> ### ** Examples
> 
> data(acid)
> 
> # fit a partial thin-plate spline
> temp <- ssr(ph~t1+x1+x2, rk=tp(t1), data=acid, spar="m")
At line 1992 of file rkpk1.f
Fortran runtime error: Index '2' of dimension 1 of array 'jpvt' above upper bound of 1
Package in Depends field not imported from: 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CALPHA: no visible global function definition for 'dbinom'
CALPHA: no visible global function definition for 'pchisq'
CAST: no visible global function definition for 'fisher.test'
CAST: no visible global function definition for 'chisq.test'
CMC: no visible global function definition for 'pf'
MULTI: no visible global function definition for 'complete.cases'
RVT1: no visible global function definition for 'pchisq'
RVT2: no visible global function definition for 'pchisq'
RWAS: no visible global function definition for 'pnorm'
SKAT: no visible global function definition for 'dbeta'
SKAT: no visible global function definition for 'pchisq'
TTEST: no visible global function definition for 'complete.cases'
TTEST: no visible global function definition for 'pf'
WST: no visible global function definition for 'mvfft'
WST: no visible global function definition for 'pnorm'
my_cmc_method: no visible global function definition for
  'complete.cases'
my_getUV: no visible global function definition for 'complete.cases'
my_orwss_method: no visible global function definition for 'sd'
my_rarecov_method: no visible global function definition for
  'chisq.test'
my_rbt_method: no visible global function definition for 'ppois'
my_score_method: no visible global function definition for 'pchisq'
my_ssu_method: no visible global function definition for 'pchisq'
my_ssuw_method: no visible global function definition for 'pchisq'
my_sum_method: no visible global function definition for 'pchisq'
my_uminp_method: no visible global function definition for 'pchisq'
my_uminp_method: no visible global function definition for 'pmvnorm'
Undefined global functions or variables:
  chisq.test complete.cases dbeta dbinom fisher.test mvfft pchisq pf
  pmvnorm pnorm ppois sd
Consider adding
  importFrom("stats", "chisq.test", "complete.cases", "dbeta", "dbinom",
             "fisher.test", "mvfft", "pchisq", "pf", "pnorm", "ppois",
             "sd")
to your NAMESPACE file.
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.
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 in Depends field not imported from:
  'cairoDevice' 'gWidgetsRGtk2' 'partitions' 'proto'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 'plot'
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 plot pnorm points printCoefmat qnorm
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
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 'plot'
plotmcmc: no visible global function definition for 'lines'
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf plot png quantile rnorm
  runif sd var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
LHSdesign: no visible global function definition for 'qnorm'
LHSdesign: no visible global function definition for 'qunif'
LHSdesign: no visible global function definition for 'qt'
MCdesign: no visible global function definition for 'rnorm'
MCdesign: no visible global function definition for 'runif'
MCdesign: no visible global function definition for 'rt'
Undefined global functions or variables:
  qnorm qt qunif rnorm rt runif
Consider adding
  importFrom("stats", "qnorm", "qt", "qunif", "rnorm", "rt", "runif")
to your NAMESPACE file.
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.
attribrisk: no visible global function definition for 'terms'
attribrisk: no visible global function definition for '.getXlevels'
attribrisk: no visible global function definition for 'model.response'
attribrisk: no visible global function definition for 'model.weights'
attribrisk: no visible global function definition for 'model.offset'
attribrisk: no visible global function definition for 'model.matrix'
attribrisk: no visible global function definition for 'model.frame'
attribrisk.fit: no visible global function definition for 'glm.fit'
attribrisk.fit: no visible global function definition for 'binomial'
attribrisk.fit: no visible global function definition for 'glm.control'
attribrisk.fit: no visible global function definition for 'coef'
attribrisk.fit: no visible global function definition for
  'coefficients'
attribrisk_boot: no visible global function definition for 'var'
print.attribrisk: no visible global function definition for 'qnorm'
summary.attribrisk: no visible global function definition for 'hasArg'
summary.attribrisk: no visible global function definition for 'var'
Undefined global functions or variables:
  .getXlevels binomial coef coefficients glm.control glm.fit hasArg
  model.frame model.matrix model.offset model.response model.weights
  qnorm terms var
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", ".getXlevels", "binomial", "coef", "coefficients",
             "glm.control", "glm.fit", "model.frame", "model.matrix",
             "model.offset", "model.response", "model.weights", "qnorm",
             "terms", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plot.AUC: no visible global function definition for 'plot'
plot.AUC: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot
Consider adding
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
AUCRFcv: no visible global function definition for 'predict'
plot.AUCRF: no visible global function definition for 'par'
plot.AUCRF: no visible global function definition for 'dotchart'
plot.AUCRF: no visible global function definition for 'title'
plot.AUCRF: no visible global function definition for 'text'
Undefined global functions or variables:
  dotchart par predict text title
Consider adding
  importFrom("graphics", "dotchart", "par", "text", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RJSONIO' 'hexbin' 'plotrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
audioHist: no visible global function definition for 'hist'
audioHist: no visible global function definition for 'rescale'
audioHist: no visible global function definition for 'toJSON'
audioScatter: no visible binding for global variable 'formula'
audioScatter: no visible global function definition for 'hexbinplot'
audioScatter: no visible global function definition for 'cor'
audioScatter: no visible global function definition for 'toJSON'
audioSplom: no visible global function definition for 'hexplom'
audioSplom: no visible binding for global variable 'BTY'
audioSplom: no visible binding for global variable 'panel.hexboxplot'
audioSplom: no visible global function definition for 'combn'
audioSplom : <anonymous>: no visible global function definition for
  'cor'
audioSplom : <anonymous>: no visible global function definition for
  'toJSON'
audiolyzRcheck: no visible global function definition for
  'download.file'
audiolyzRcheck: no visible global function definition for 'unzip'
matricize: no visible global function definition for 'hexbin'
panel.audiolyzR: no visible global function definition for
  'panel.hexbinplot'
Undefined global functions or variables:
  BTY combn cor download.file formula hexbin hexbinplot hexplom hist
  panel.hexbinplot panel.hexboxplot rescale toJSON unzip
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "formula")
  importFrom("utils", "combn", "download.file", "unzip")
to your NAMESPACE file.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/audio.Rcheck/00install.out' for details.
simulateD: no visible global function definition for 'rgamma'
simulateT: no visible global function definition for 'runif'
simulateT: no visible global function definition for 'rbeta'
simulateT: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbeta rbinom rgamma runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rgamma", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'rPython'
'library' or 'require' calls in package code:
  'ggplot2' 'gpclib' 'maptools'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
gLog.ep: no visible global function definition for 'quantile'
gedestp: no visible global function definition for 'na.omit'
gedestp: no visible global function definition for 'optim'
gets.mean: no visible global function definition for 'start'
gets.mean: no visible global function definition for 'end'
gets.mean: no visible global function definition for 'window'
gets.mean: no visible global function definition for 'pt'
gets.mean: no visible global function definition for 'Box.test'
gets.mean: no visible global function definition for 'pchisq'
gets.vol: no visible global function definition for 'start'
gets.vol: no visible global function definition for 'end'
gets.vol: no visible global function definition for 'window'
gets.vol: no visible global function definition for 'pt'
gets.vol: no visible global function definition for 'Box.test'
gets.vol: no visible global function definition for 'pchisq'
jb.test: no visible global function definition for 'pchisq'
skewness.test: no visible global function definition for 'pchisq'
sm: no visible global function definition for 'start'
sm: no visible global function definition for 'end'
sm: no visible global function definition for 'window'
sm: no visible global function definition for 'pt'
sm: no visible global function definition for 'pchisq'
sm: no visible global function definition for 'Box.test'
Undefined global functions or variables:
  Box.test end na.omit optim pchisq pt quantile start window
Consider adding
  importFrom("stats", "Box.test", "end", "na.omit", "optim", "pchisq",
             "pt", "quantile", "start", "window")
to your NAMESPACE file.
CRexp_set: no visible global function definition for 'runif'
b6e6rl: no visible global function definition for 'runif'
derand_RL: no visible global function definition for 'runif'
derandexp_RL: no visible global function definition for 'runif'
nahvyb_expt: no visible global function definition for 'runif'
roulete: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.generateTransform: no visible global function definition for 'sd'
.generateUnitHyperCube: no visible global function definition for
  'runif'
.makeBoundedSingleStep: no visible global function definition for
  'runif'
.makeBoundedStep: no visible global function definition for 'runif'
.makeStep: no visible global function definition for 'runif'
.staircaseSampling: no visible global function definition for 'runif'
GaussianPrior: no visible global function definition for 'qnorm'
LogNormalPrior: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
    libs   1.8Mb
BACprior.CV: no visible global function definition for 'na.fail'
BACprior.CV: no visible global function definition for 'plot'
BACprior.CV: no visible global function definition for 'abline'
BACprior.boot: no visible global function definition for 'na.fail'
BACprior.boot: no visible global function definition for 'plot'
BACprior.boot: no visible global function definition for 'abline'
BACprior.lm: no visible global function definition for 'na.fail'
BACprior.lm: no visible global function definition for 'coef'
BACprior.lm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  abline coef na.fail plot vcov
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
bagging: no visible global function definition for 'predict'
samme: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Running 'test-all.R' [1s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > library(bagRboostR)
  > 
  > test_package("bagRboostR")
  -- 1. Error: samme returns a character vector of predicted classes (@test_samme.
  Need at least two classes to do classification.
  1: samme(activity ~ ., train, test, 3, ntree = 5, trace = F) at D:/temp/RtmpcNQlre/RLIBS_1105458e13b8/bagRboostR/tests/test_samme.R:6
  2: randomForest(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  3: randomForest.formula(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  4: randomForest.default(m, y, ...)
  5: stop("Need at least two classes to do classification.")
  
  == testthat results  ===========================================================
  OK: 39 SKIPPED: 0 FAILED: 1
  1. Error: samme returns a character vector of predicted classes (@test_samme.R#6) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
best_binomial_bandit : f: no visible global function definition for
  'dbeta'
best_binomial_bandit : f: no visible global function definition for
  'pbeta'
best_binomial_bandit: no visible global function definition for
  'integrate'
best_poisson_bandit : f: no visible global function definition for
  'dgamma'
best_poisson_bandit : f: no visible global function definition for
  'pgamma'
best_poisson_bandit: no visible global function definition for
  'integrate'
deseasonalized_trend: no visible global function definition for
  'predict'
distribution_estimate: no visible global function definition for
  'quantile'
distribution_estimate: no visible global function definition for
  'qbeta'
significance_analysis: no visible global function definition for
  'prop.test'
sim_post: no visible global function definition for 'rbeta'
summarize_metrics: no visible global function definition for 'median'
summarize_metrics: no visible global function definition for
  'prop.test'
Undefined global functions or variables:
  dbeta dgamma integrate median pbeta pgamma predict prop.test qbeta
  quantile rbeta
Consider adding
  importFrom("stats", "dbeta", "dgamma", "integrate", "median", "pbeta",
             "pgamma", "predict", "prop.test", "qbeta", "quantile",
             "rbeta")
to your NAMESPACE file.
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
extractAffybatch: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls to packages already attached by Depends:
  'grid' 'lattice'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'grid' 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
barcode: no visible global function definition for 'unit'
barcode: no visible global function definition for 'grid.newpage'
barcode: no visible global function definition for 'grid.text'
barcode: no visible global function definition for 'gpar'
barcode: no visible global function definition for 'pushViewport'
barcode: no visible global function definition for 'viewport'
barcode: no visible global function definition for 'convertHeight'
barcode: no visible global function definition for 'convertWidth'
barcode: no visible global function definition for 'grid.rect'
barcode: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for 'unit'
barcode.panel: no visible global function definition for 'hist'
barcode.panel: no visible global function definition for 'pushViewport'
barcode.panel: no visible global function definition for 'viewport'
barcode.panel: no visible global function definition for 'grid.xaxis'
barcode.panel: no visible global function definition for 'gpar'
barcode.panel: no visible global function definition for 'grid.text'
barcode.panel: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for
  'grid.segments'
barcode.panel: no visible global function definition for 'grid.points'
Undefined global functions or variables:
  convertHeight convertWidth gpar grid.newpage grid.points grid.rect
  grid.segments grid.text grid.xaxis hist popViewport pushViewport unit
  viewport
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
    libs   1.9Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Packages which this enhances but not available for checking:
  'doMC' 'rPython'
'library' or 'require' call to 'hwriter' which was already attached by Depends.
  Please remove these calls from your code.
Package suggested but not available for checking: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/BayClone2.Rcheck/00install.out' for details.
'library' or 'require' call not declared from: 'foreach'
FECRT: no visible global function definition for 'pdf'
FECRT: no visible global function definition for 'hist'
FECRT: no visible global function definition for 'abline'
FECRT: no visible global function definition for 'dev.off'
FECRT.analysis: no visible global function definition for 'pdf'
FECRT.analysis: no visible global function definition for 'hist'
FECRT.analysis: no visible global function definition for 'abline'
FECRT.analysis: no visible global function definition for 'dev.off'
fecrt: no visible global function definition for 'pdf'
fecrt: no visible global function definition for 'hist'
fecrt: no visible global function definition for 'abline'
fecrt: no visible global function definition for 'dev.off'
fecrt.analysis: no visible global function definition for 'pdf'
fecrt.analysis: no visible global function definition for 'hist'
fecrt.analysis: no visible global function definition for 'abline'
fecrt.analysis: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline dev.off hist pdf
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "hist")
to your NAMESPACE file.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.1Mb
BMAnimalTrack: no visible global function definition for 'nlm'
BMAnimalTrack: no visible global function definition for 'qnorm'
dataSim: no visible global function definition for 'rnorm'
rBBridge: no visible global function definition for 'rnorm'
rBMotion: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  nlm qnorm rnorm
Consider adding
  importFrom("stats", "nlm", "qnorm", "rnorm")
to your NAMESPACE file.
BayesianbetaregEst: no visible global function definition for 'runif'
BayesianbetaregEst: no visible global function definition for 'as.ts'
BayesianbetaregEst: no visible global function definition for 'dev.new'
BayesianbetaregEst: no visible global function definition for 'ts.plot'
BayesianbetaregEst: no visible binding for global variable 'sd'
BayesianbetaregEst: no visible global function definition for
  'quantile'
betaresiduals : lt: no visible global function definition for 'dbeta'
diagnostics: no visible global function definition for 'plot'
diagnostics: no visible global function definition for 'abline'
diagnostics: no visible global function definition for 'qqnorm'
diagnostics: no visible global function definition for 'qqline'
dpostb: no visible global function definition for 'dbeta'
dpostg: no visible global function definition for 'dbeta'
plotresiduals: no visible global function definition for 'plot'
print.summary.Bayesianbetareg: no visible global function definition
  for 'printCoefmat'
summary.Bayesianbetareg: no visible global function definition for
  'coef'
Undefined global functions or variables:
  abline as.ts coef dbeta dev.new plot printCoefmat qqline qqnorm
  quantile runif sd ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "as.ts", "coef", "dbeta", "printCoefmat", "qqline",
             "qqnorm", "quantile", "runif", "sd", "ts.plot")
to your NAMESPACE file.
'library' or 'require' call not declared from: 'Matching'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.0Mb
    libs   2.1Mb
NeedsCompilation field should likely be 'yes'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   4.0Mb
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.
MHratioPopPref: no visible global function definition for 'runif'
MratioPopMult: no visible global function definition for 'dunif'
MratioPopMult: no visible global function definition for 'runif'
bayesPref: no visible global function definition for 'runif'
calcP: no visible global function definition for 'dunif'
calcP: no visible global function definition for 'dmultinom'
calcdic: no visible global function definition for 'median'
calcdic: no visible binding for global variable 'median'
calcdic: no visible global function definition for 'dmultinom'
calcdicExtern: no visible global function definition for 'median'
calcdicExtern: no visible global function definition for 'dmultinom'
calcdicExtern: no visible binding for global variable 'median'
credibleIntervals: no visible global function definition for 'quantile'
prefPlot: no visible global function definition for 'postscript'
prefPlot: no visible global function definition for 'plot'
prefPlot: no visible global function definition for 'lines'
prefPlot: no visible global function definition for 'density'
prefPlot: no visible global function definition for 'median'
prefPlot: no visible global function definition for 'legend'
prefPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median plot postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
mlike.alt.g.AR: no visible global function definition for 'integrate'
mlike.alt.gtheta.AR: no visible global function definition for 'dbeta'
mlike.null.AR: no visible global function definition for 'dbeta'
multilevel.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
multilevel.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
trendtest.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.Gibbs.AR: no visible global function definition for 'dcauchy'
trendtest.Gibbs.AR: no visible global function definition for 'pcauchy'
trendtest.MC.AR: no visible global function definition for
  'txtProgressBar'
trendtest.MC.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.nullMargLikeAR: no visible global function definition for
  'integrate'
ttest.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
ttest.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
ttest.Gibbs.AR: no visible global function definition for 'dcauchy'
ttest.Gibbs.AR: no visible global function definition for 'pcauchy'
ttest.MCGQ.AR: no visible global function definition for 'integrate'
Undefined global functions or variables:
  dbeta dcauchy integrate pcauchy setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "dbeta", "dcauchy", "integrate", "pcauchy")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'combinat' 'gplots' 'mnormt'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bayes.regress: no visible binding for global variable 'var'
bayesregressB1S1: no visible global function definition for 'rgamma'
bayesregressB1S2: no visible global function definition for 'rgamma'
bayesregressB2S1: no visible global function definition for 'rgamma'
bayesregressB2S2: no visible global function definition for 'rgamma'
bayesregressB3S1: no visible global function definition for 'rWishart'
bayesregressB3S1: no visible global function definition for 'rgamma'
bayesregressB3S2: no visible global function definition for 'rWishart'
bayesregressB3S2: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rWishart rgamma var
Consider adding
  importFrom("stats", "rWishart", "rgamma", "var")
to your NAMESPACE file.
validate: no visible binding for global variable 'qnorm'
validate: no visible global function definition for 'pchisq'
validate: no visible global function definition for 'qnorm'
validate: no visible global function definition for 'plot'
validate: no visible global function definition for 'axis'
validate: no visible global function definition for 'points'
validate: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis pchisq plot points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
Unexported object imported by a ':::' call: 'boa:::boa.getparms'
  See the note in ?`:::` about the use of this operator.
File 'BayHap/libs/i386/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'
File 'BayHap/libs/x64/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'coda' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'mvnmle' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
BilogData: no visible global function definition for 'write.table'
CohensD.rawData: no visible global function definition for 'var'
EtaSq: no visible global function definition for 'summary.aov'
HedgesG.rawData: no visible global function definition for 'var'
LittleMCAR: no visible global function definition for 'mlest'
LittleMCAR: no visible global function definition for 'pchisq'
PseudoR2: no visible global function definition for 'predict'
Undefined global functions or variables:
  mlest pchisq predict summary.aov var write.table
Consider adding
  importFrom("stats", "pchisq", "predict", "summary.aov", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'fields' 'poibin' 'rjags'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BMR.plot: no visible global function definition for 'heat.colors'
BMR.plot: no visible global function definition for 'image.plot'
BMR.plot: no visible global function definition for 'title'
BMR.plot: no visible global function definition for 'mtext'
BMR.plot: no visible global function definition for 'par'
baysic.data: no visible global function definition for 'layout'
baysic.data: no visible global function definition for 'barplot'
baysic.data: no visible global function definition for 'rainbow'
baysic.fit: no visible global function definition for 'jags.model'
baysic.fit: no visible global function definition for 'update'
baysic.fit: no visible global function definition for 'coda.samples'
baysic.test: no visible global function definition for 'ppois'
baysic.test : <anonymous>: no visible global function definition for
  'ppoibin'
baysic.test: no visible global function definition for 'pbinom'
fuzzy.FDR.approx: no visible global function definition for 'p.adjust'
fuzzy.FDR.approx: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot coda.samples heat.colors image.plot jags.model layout mtext
  p.adjust par pbinom ppoibin ppois rainbow runif title update
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "layout", "mtext", "par", "title")
  importFrom("stats", "p.adjust", "pbinom", "ppois", "runif", "update")
to your NAMESPACE file.
BAYSTAR: no visible global function definition for 'median'
BAYSTAR: no visible global function definition for 'ar'
BAYSTAR: no visible global function definition for 'quantile'
BAYSTAR: no visible global function definition for 'dev.new'
BAYSTAR: no visible global function definition for 'ts.plot'
BAYSTAR: no visible global function definition for 'title'
BAYSTAR: no visible global function definition for 'par'
BAYSTAR: no visible global function definition for 'plot.ts'
BAYSTAR: no visible global function definition for 'lines'
BAYSTAR: no visible global function definition for 'acf'
TAR.lagd: no visible global function definition for 'runif'
TAR.sigma: no visible global function definition for 'rgamma'
TAR.simu: no visible global function definition for 'rnorm'
TAR.summary: no visible global function definition for 'quantile'
TAR.summary: no visible global function definition for 'sd'
TAR.thres: no visible global function definition for 'rnorm'
TAR.thres: no visible global function definition for 'runif'
Undefined global functions or variables:
  acf ar dev.new lines median par plot.ts quantile rgamma rnorm runif
  sd title ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "lines", "par", "title")
  importFrom("stats", "acf", "ar", "median", "plot.ts", "quantile",
             "rgamma", "rnorm", "runif", "sd", "ts.plot")
to your NAMESPACE file.
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.
LaplaceMetropolis_admkr: no visible binding for global variable
  'median'
LaplaceMetropolis_admkr: no visible global function definition for
  'mad'
LaplaceMetropolis_gaussian: no visible binding for global variable
  'median'
LaplaceMetropolis_gaussian: no visible global function definition for
  'mad'
cost_admkr: no visible global function definition for 'sd'
cov_chol: no visible global function definition for 'qchisq'
cov_chol_admkr: no visible global function definition for 'qchisq'
gibbs_admkr_erro: no visible global function definition for 'rnorm'
gibbs_admkr_erro: no visible global function definition for 'runif'
gibbs_admkr_nw: no visible global function definition for 'qnorm'
gibbs_admkr_nw: no visible global function definition for 'rnorm'
gibbs_admkr_nw: no visible global function definition for 'runif'
loglikelihood_admkr: no visible global function definition for 'sd'
margin_like_admkr: no visible global function definition for 'sd'
np_gibbs: no visible global function definition for 'qnorm'
np_gibbs: no visible global function definition for 'rnorm'
np_gibbs: no visible global function definition for 'runif'
np_gibbs: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  mad median qchisq qnorm rgamma rnorm runif sd
Consider adding
  importFrom("stats", "mad", "median", "qchisq", "qnorm", "rgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
bbmm.contour: no visible global function definition for 'na.omit'
bbmm.contour: no visible global function definition for 'optimize'
bbmm.contour: no visible global function definition for 'contour'
bbmm.contour: no visible global function definition for 'points'
bbmm.contour: no visible global function definition for 'lines'
brownian.bridge: no visible global function definition for 'sd'
brownian.motion.variance: no visible global function definition for
  'optimize'
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
bbo: no visible global function definition for 'runif'
bbo: no visible global function definition for 'tail'
plot.bbo: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'HI' 'lme4' 'locfit' 'secr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BBRecap: no visible global function definition for 'optimize'
BBRecap: no visible global function definition for 'arms'
BBRecap: no visible global function definition for 'median'
BBRecap : HPD.interval: no visible global function definition for
  'density'
BBRecap : HPD.interval: no visible global function definition for
  'quantile'
BBRecap.custom.part: no visible global function definition for
  'optimize'
LBRecap: no visible global function definition for 'findbars'
LBRecap: no visible global function definition for 'as.formula'
LBRecap: no visible global function definition for 'glm'
LBRecap: no visible global function definition for 'binomial'
LBRecap: no visible global function definition for 'glmer'
LBRecap: no visible global function definition for 'logLik'
LBRecap: no visible global function definition for 'coef'
LBRecap: no visible global function definition for 'na.omit'
LBRecap: no visible global function definition for 'fixef'
LBRecap: no visible global function definition for 'ranef'
LBRecap: no visible global function definition for 'qnorm'
LBRecap: no visible global function definition for 'plot'
LBRecap: no visible global function definition for 'points'
LBRecap: no visible global function definition for 'axis'
LBRecap: no visible global function definition for 'abline'
LBRecap.custom.part: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  abline arms as.formula axis binomial coef density findbars fixef glm
  glmer logLik median na.omit optimize plot points qnorm quantile ranef
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "as.formula", "binomial", "coef", "density", "glm",
             "logLik", "median", "na.omit", "optimize", "qnorm",
             "quantile")
to your NAMESPACE file.
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
pairs.bce : panel.cor: no visible global function definition for 'text'
pairs.bce : panel.cor: no visible global function definition for 'cor'
pairs.bce : panel.hist: no visible global function definition for 'par'
pairs.bce : panel.hist: no visible global function definition for
  'hist'
pairs.bce : panel.hist: no visible global function definition for
  'rect'
pairs.bce: no visible global function definition for 'pairs'
panel.cor: no visible global function definition for 'par'
panel.cor: no visible global function definition for 'cor'
panel.cor: no visible global function definition for 'strwidth'
panel.cor: no visible global function definition for 'text'
rdirichlet2: no visible global function definition for 'rgamma'
summary.bce: no visible global function definition for 'cov'
summary.bce: no visible binding for global variable 'sd'
summary.bce: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  cor cov hist pairs par quantile rect rgamma sd strwidth text
Consider adding
  importFrom("graphics", "hist", "pairs", "par", "rect", "strwidth",
             "text")
  importFrom("stats", "cor", "cov", "quantile", "rgamma", "sd")
to your NAMESPACE file.
Packages suggested but not available for checking: 'bcmaps.rdata' 'doMC'
plot.cvsvd: no visible binding for global variable 'sd'
plot.cvsvd: no visible global function definition for 'plot'
plot.cvsvd: no visible global function definition for 'lines'
plot.cvsvd: no visible global function definition for 'segments'
plot.cvsvd: no visible global function definition for 'points'
print.cvsvd: no visible binding for global variable 'sd'
summary.cvsvd: no visible binding for global variable 'sd'
Undefined global functions or variables:
  lines plot points sd segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
mise: no visible global function definition for 'integrate'
density,BrVitale : density.vitale : <anonymous>: no visible global
  function definition for 'dbeta'
density,Chen99Kernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,HirukawaJLNKernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,MicroBetaChen99Kernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,Vitale : <anonymous>: no visible global function definition for
  'dbeta'
distribution,BernsteinPolynomials : <anonymous>: no visible global
  function definition for 'integrate'
distribution,KernelDensity : <anonymous>: no visible global function
  definition for 'integrate'
print,BoundedDensity: no visible global function definition for 'str'
print,KernelDensity: no visible global function definition for 'str'
rsample,BoundedDensity: no visible global function definition for
  'runif'
setNormalizationConst,MacroBetaChen99Kernel: no visible global function
  definition for 'integrate'
setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global
  function definition for 'integrate'
setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global
  function definition for 'integrate'
setNormalizationConstants,MicroBetaChen99Kernel :
  density.kernelFunction: no visible global function definition for
  'dbeta'
setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no
  visible global function definition for 'integrate'
show,BoundedDensity: no visible global function definition for 'str'
show,KernelDensity: no visible global function definition for 'str'
Undefined global functions or variables:
  dbeta integrate runif str
Consider adding
  importFrom("stats", "dbeta", "integrate", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
BDtest: no visible global function definition for 'binom.test'
CIlnpv: no visible global function definition for 'qnorm'
CIlnpvak: no visible global function definition for 'qnorm'
CIlppv: no visible global function definition for 'qnorm'
CIlppvak: no visible global function definition for 'qnorm'
CIpvBI: no visible global function definition for 'rbeta'
CIpvBI: no visible global function definition for 'quantile'
CIpvBI: no visible global function definition for 'median'
CIpvBII: no visible global function definition for 'rbeta'
CIpvBII: no visible global function definition for 'quantile'
CIpvBII: no visible global function definition for 'median'
nNPV: no visible global function definition for 'qnorm'
nPPV: no visible global function definition for 'qnorm'
plotnPV: no visible global function definition for 'na.omit'
plotnPV: no visible global function definition for 'lines'
plotnPV2 : defplot: no visible global function definition for 'plot'
plotnPV2 : defplot: no visible global function definition for 'lines'
plotnPV2: no visible global function definition for 'par'
plotnPV2: no visible global function definition for 'layout'
simPV: no visible global function definition for 'rbinom'
simPV: no visible global function definition for 'quantile'
Undefined global functions or variables:
  binom.test layout lines median na.omit par plot qnorm quantile rbeta
  rbinom
Consider adding
  importFrom("graphics", "layout", "lines", "par", "plot")
  importFrom("stats", "binom.test", "median", "na.omit", "qnorm",
             "quantile", "rbeta", "rbinom")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RColorBrewer' 'beadarray'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
beadtypeFilter: no visible global function definition for 'na.omit'
beadtypeFilter: no visible global function definition for 'exprs'
beadtypeFilter: no visible global function definition for 'se.exprs'
beadtypeFilter: no visible global function definition for 'beadNum'
beadtypeFilter: no visible global function definition for 'fData'
emCDF: no visible global function definition for 'brewer.pal'
emCDF: no visible global function definition for 'plot'
emCDF: no visible global function definition for 'ecdf'
emCDF: no visible global function definition for 'legend'
emCDF: no visible global function definition for 'lines'
emCDF: no visible global function definition for 'text'
emCDF: no visible global function definition for 'reshape'
iccFun : <anonymous>: no visible global function definition for
  'quantile'
varianceplot: no visible global function definition for 'reshape'
varianceplot: no visible global function definition for 'plot'
varianceplot: no visible global function definition for 'points'
varianceplot: no visible global function definition for 'legend'
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit plot points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
'library' or 'require' call to 'multcomp' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
beqi2: no visible global function definition for 'na.omit'
beqi2: no visible global function definition for 'browseURL'
readAMBI: no visible global function definition for 'read.csv'
readBEQI: no visible global function definition for 'read.csv'
readERF: no visible global function definition for 'read.csv'
readTWN: no visible global function definition for 'read.csv'
read_ITI_FIBI: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  browseURL na.omit read.csv
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "read.csv")
to your NAMESPACE file.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
ber: no visible global function definition for 'model.matrix'
ber: no visible global function definition for 'as.formula'
ber_bg: no visible global function definition for 'model.matrix'
ber_bg: no visible global function definition for 'as.formula'
combat_np: no visible global function definition for 'as.formula'
combat_np: no visible global function definition for 'model.matrix'
combat_p: no visible global function definition for 'as.formula'
combat_p: no visible global function definition for 'model.matrix'
combat_p: no visible binding for global variable 'var'
combat_p: no visible global function definition for 'par'
combat_p: no visible global function definition for 'density'
combat_p: no visible global function definition for 'plot'
combat_p: no visible global function definition for 'lines'
combat_p: no visible global function definition for 'dnorm'
combat_p: no visible global function definition for 'qqnorm'
combat_p: no visible global function definition for 'qqline'
combat_p: no visible global function definition for 'rgamma'
combat_p: no visible global function definition for 'qqplot'
combat_p: no visible global function definition for 'title'
mean_centering: no visible global function definition for
  'model.matrix'
standardization: no visible global function definition for
  'model.matrix'
Undefined global functions or variables:
  as.formula density dnorm lines model.matrix par plot qqline qqnorm
  qqplot rgamma title var
Consider adding
  importFrom("graphics", "lines", "par", "plot", "title")
  importFrom("stats", "as.formula", "density", "dnorm", "model.matrix",
             "qqline", "qqnorm", "qqplot", "rgamma", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'Rmpfr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bI: no visible global function definition for 'is'
bI: no visible global function definition for 'mpfr'
bI: no visible binding for global variable 'slot'
bI: no visible global function definition for 'as'
Undefined global functions or variables:
  as is mpfr slot
Consider adding
  importFrom("methods", "as", "is", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
betafam: no visible global function definition for 'pnorm'
betafam: no visible global function definition for 'pchisq'
betafam: no visible global function definition for 'lm'
betafam: no visible global function definition for 'coefficients'
betafam: no visible global function definition for 'glm.fit'
betafam: no visible global function definition for 'gaussian'
betafam: no visible global function definition for 'glmnet'
Undefined global functions or variables:
  coefficients gaussian glm.fit glmnet lm pchisq pnorm
Consider adding
  importFrom("stats", "coefficients", "gaussian", "glm.fit", "lm",
             "pchisq", "pnorm")
to your NAMESPACE file.
Checking should be performed on sources prepared by 'R CMD build'.
'library' or 'require' call to 'vegan' which was already attached by Depends.
  Please remove these calls from your code.
S3 methods shown with full name in documentation object 'cca.pertables':
  'cca.pertables'

S3 methods shown with full name in documentation object 'rda.pertables':
  'rda.pertables'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
betas.lm: no visible binding for global variable 'sd'
betas.lm: no visible global function definition for 'sd'
my.wtd.var: no visible global function definition for 'var'
Undefined global functions or variables:
  sd var
Consider adding
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
bezierArcLength: no visible global function definition for 'sd'
bezierArcLength: no visible global function definition for 'lm'
bezierCurveFit: no visible global function definition for 'nls'
bezierCurveFit: no visible global function definition for 'nls.control'
bezierCurveFit: no visible global function definition for 'lm'
bezierCurveFit: no visible global function definition for 'na.omit'
pointsOnBezier: no visible global function definition for 'optim'
Undefined global functions or variables:
  lm na.omit nls nls.control optim sd
Consider adding
  importFrom("stats", "lm", "na.omit", "nls", "nls.control", "optim",
             "sd")
to your NAMESPACE file.
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.
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.
installed size is 141.1Mb
  sub-directories of 1Mb or more:
    include  140.1Mb
Package in Depends field not imported from: 'betareg'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bias: no visible global function definition for 'predict'
bias: no visible global function definition for 'pnorm'
bias: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  model.matrix pnorm predict
Consider adding
  importFrom("stats", "model.matrix", "pnorm", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:145:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:153:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:178:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:180:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/3.6/bigalgebra.Rcheck/00install.out' for details.
anon_matrix: no visible global function definition for
  'filebacked.big.matrix'
anon_matrix: no visible global function definition for 'capture.output'
finalize_anon_matrix: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output filebacked.big.matrix
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:145:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:153:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:178:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:180:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/3.6/biganalytics.Rcheck/00install.out' for details.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:145:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:153:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:178:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:180:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/3.6/bigFastlm.Rcheck/00install.out' for details.
Packages in Depends field not imported from:
  'DBI' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bigglm.RODBC: no visible global function definition for 'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'sqlGetResults'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbSendQuery'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbSendQuery'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'fetch'
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:145:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:153:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:178:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:180:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/3.6/bigmemory.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'synchronicity'
Package unavailable to check Rd xrefs: 'synchronicity'
quickModel: no visible global function definition for 'tail'
quickSource: no visible global function definition for 'write.table'
Undefined global functions or variables:
  tail write.table
Consider adding
  importFrom("utils", "tail", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:145:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:153:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:178:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:180:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/3.6/bigtabulate.Rcheck/00install.out' for details.
Packages in Depends field not imported from:
  'gbm' 'glmnet' 'randomForest' 'tree'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LDCAEst: no visible global function definition for 'glmnet'
cv.LDCA: no visible global function definition for 'cv.glmnet'
predict.LDCA: no visible global function definition for 'predict'
predict.cv.LDCA: no visible global function definition for 'predict'
predict.tsp.gbm: no visible global function definition for 'predict'
predict.tsp.randomForest: no visible global function definition for
  'predict'
predict.tsp.tree: no visible global function definition for 'predict'
tsp.gbm: no visible global function definition for 'gbm.fit'
tsp.randomForest: no visible global function definition for
  'randomForest'
tsp.tree: no visible global function definition for 'tree.control'
tsp.tree: no visible global function definition for 'tree'
Undefined global functions or variables:
  cv.glmnet gbm.fit glmnet predict randomForest tree tree.control
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.2Mb
plot,bild-missing: no visible global function definition for
  'dev.interactive'
plot,bild-missing: no visible global function definition for
  'devAskNewPage'
plot,bild-missing: no visible global function definition for
  'extendrange'
Undefined global functions or variables:
  dev.interactive devAskNewPage extendrange
Consider adding
  importFrom("grDevices", "dev.interactive", "devAskNewPage",
             "extendrange")
to your NAMESPACE file.
chisq.sim.factory : chisq.sim.func: no visible global function
  definition for 'chisq.test'
rmultnom: no visible global function definition for 'runif'
Undefined global functions or variables:
  chisq.test runif
Consider adding
  importFrom("stats", "chisq.test", "runif")
to your NAMESPACE file.
commonprob2sigma: no visible global function definition for 'approxfun'
rmvbin: no visible global function definition for 'qnorm'
simul.commonprob: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  approxfun qnorm
Consider adding
  importFrom("stats", "approxfun", "qnorm")
to your NAMESPACE file.
bin_ps: no visible global function definition for 'runif'
bin_ps: no visible global function definition for 'dbinom'
draw_i: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbinom runif
Consider adding
  importFrom("stats", "dbinom", "runif")
to your NAMESPACE file.
IndivdRUMIndMH: no visible global function definition for
  'flush.console'
dRUMAuxMix: no visible global function definition for 'flush.console'
dRUMHAM: no visible global function definition for 'flush.console'
dRUMIndMH: no visible global function definition for 'flush.console'
print.binomlogit: no visible global function definition for 'is'
summary.binomlogit: no visible global function definition for 'is'
Undefined global functions or variables:
  flush.console is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'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.
bins.quantiles: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package suggested but not available for checking: 'BiocVersion'
'library' or 'require' calls to packages already attached by Depends:
  'ape' 'cladoRcpp' 'phylobase' 'rexpokit'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'ape' 'cladoRcpp' 'methods' 'phylobase' 'rexpokit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'ape:::floating.pie.asp' 'cladoRcpp:::areas_list_to_states_list_old'
  See the note in ?`:::` about the use of this operator.
Running examples in 'BioInstaller-Ex.R' failed
The error most likely occurred in:

> ### Name: install.bioinfo
> ### Title: Download and install biology software or database
> ### Aliases: install.bioinfo
> 
> ### ** Examples
> 
> db <- sprintf('%s/.BioInstaller', tempdir())
> set.biosoftwares.db(db)
> install.bioinfo('bwa', show.all.versions = TRUE)
INFO [2018-06-25 19:53:46] Fetching bwa versions....
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: install.bioinfo ... github2versions -> getURL -> curlPerform -> <Anonymous> -> fun
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 46-70 (BioInstaller.Rmd) 
Error: processing vignette 'BioInstaller.Rmd' failed with diagnostics:
error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Execution halted
'library' or 'require' call not declared from: 'magrittr'
Missing or unexported object: 'gam::step.gam'
'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.
binom.ci : bc: no visible global function definition for 'qf'
binom.ci : bc: no visible global function definition for 'qnorm'
cvar: no visible global function definition for 'sd'
eta2: no visible global function definition for 'lm'
eta2: no visible global function definition for 'as.formula'
gg_qqplot: no visible binding for global variable 'qnorm'
gg_qqplot: no visible global function definition for 'quantile'
panel.hist: no visible global function definition for 'par'
panel.hist: no visible global function definition for 'hist'
panel.hist: no visible global function definition for 'rect'
plotcdf2: no visible global function definition for 'colorRampPalette'
plotcdf2 : jet.colors: no visible global function definition for 'gray'
plotcdf2: no visible global function definition for 'persp'
poi.ci: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  as.formula colorRampPalette gray hist lm par persp qchisq qf qnorm
  quantile rect sd
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "hist", "par", "persp", "rect")
  importFrom("stats", "as.formula", "lm", "qchisq", "qf", "qnorm",
             "quantile", "sd")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.5Mb
Depends: includes the non-default packages:
  'colorspace' 'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bivarcalcn: no visible global function definition for 'qnorm'
bivarcalcn: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
biwt.cor: no visible global function definition for 'covMcd'
biwt.cor: no visible binding for global variable 'mad'
biwt.est: no visible global function definition for 'covMcd'
biwt.est: no visible global function definition for 'mahalanobis'
chi.int: no visible global function definition for 'pchisq'
chi.int.p: no visible global function definition for 'dchisq'
chi.int2: no visible global function definition for 'pchisq'
chi.int2.p: no visible global function definition for 'dchisq'
rejpt.bw: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  covMcd dchisq mad mahalanobis pchisq
Consider adding
  importFrom("stats", "dchisq", "mad", "mahalanobis", "pchisq")
to your NAMESPACE file.
Package suggested but not available for checking: 'RQuantLib'
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Package suggested but not available for checking: 'bigrf'
Missing or unexported object: 'xgboost::predict'
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'blkergm'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'blkergm'
See 'd:/Rcompile/CRANpkg/local/3.6/blkergm.Rcheck/00install.out' for details.
bglmer: no visible global function definition for 'packageVersion'
getBglmerDevianceFunctionBody: no visible global function definition
  for 'packageVersion'
getParInfo : <anonymous>: no visible global function definition for
  'sd'
makeRefitDevFun: no visible global function definition for
  'packageVersion'
mkBglmerDevfun: no visible global function definition for
  'packageVersion'
namedList: no visible global function definition for 'setNames'
refit.bmerMod: no visible global function definition for
  'packageVersion'
refit.bmerMod: no visible global function definition for 'model.frame'
refit.bmerMod: no visible global function definition for 'family'
refit.bmerMod: no visible global function definition for 'getCall'
Undefined global functions or variables:
  family getCall model.frame packageVersion sd setNames
Consider adding
  importFrom("stats", "family", "getCall", "model.frame", "sd",
             "setNames")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
blockmodelskmeans: no visible global function definition for 'dist'
matrixplot: no visible global function definition for 'image'
matrixplot: no visible global function definition for 'hsv'
matrixplot: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis dist hsv image
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "axis", "image")
  importFrom("stats", "dist")
to your NAMESPACE file.
plotblockrand: no visible global function definition for 'pdf'
plotblockrand: no visible global function definition for 'dev.off'
plotblockrand: no visible global function definition for 'par'
plotblockrand: no visible global function definition for 'plot.new'
plotblockrand: no visible global function definition for 'strheight'
plotblockrand: no visible global function definition for 'strwidth'
plotblockrand: no visible global function definition for 'text'
plotblockrand: no visible global function definition for 'lines'
Undefined global functions or variables:
  dev.off lines par pdf plot.new strheight strwidth text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot.new", "strheight",
             "strwidth", "text")
to your NAMESPACE file.
BLR: no visible global function definition for 'weighted.mean'
BLR: no visible global function definition for 'var'
BLR: no visible global function definition for 'model.matrix'
BLR: no visible global function definition for 'rnorm'
BLR: no visible global function definition for 'rchisq'
BLR: no visible global function definition for 'rgamma'
BLR: no visible global function definition for 'dnorm'
dLambda: no visible global function definition for 'dgamma'
dScaledInvChisq: no visible global function definition for 'dchisq'
metropLambda: no visible global function definition for 'rgamma'
metropLambda: no visible global function definition for 'dexp'
metropLambda: no visible global function definition for 'dbeta'
metropLambda: no visible global function definition for 'dgamma'
metropLambda: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbeta dchisq dexp dgamma dnorm model.matrix rchisq rgamma rnorm runif
  var weighted.mean
Consider adding
  importFrom("stats", "dbeta", "dchisq", "dexp", "dgamma", "dnorm",
             "model.matrix", "rchisq", "rgamma", "rnorm", "runif", "var",
             "weighted.mean")
to your NAMESPACE file.
Running examples in 'blscrapeR-Ex.R' failed
The error most likely occurred in:

> ### Name: qcew_api
> ### Title: Request data from the Quarterly Census of Employment and Wages.
> ### Aliases: qcew_api
> ### Keywords: api bls cpi economics inflation unemployment
> 
> ### ** Examples
> 
> 
> # A request for the employment levels and wages for NIACS 5112: Software Publishers.
> dat <- qcew_api(year=2015, qtr="A", slice="area", sliceCode="US000")
Please set a numeric year.
Trying BLS servers...
URL caused a warning. Please check your parameters and try again: https://data.bls.gov/cew/data/api/2015/A/area/US000.csv
Error in qcew_api(year = 2015, qtr = "A", slice = "area", sliceCode = "US000") : 
  object 'qcewDat' not found
Execution halted
Package in Depends field not imported from: 'drc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bmd: no visible global function definition for 'qnorm'
bmd: no visible global function definition for 'predict'
bmd: no visible global function definition for 'LL.2'
bmd: no visible global function definition for 'LN.2'
bmd: no visible global function definition for 'W1.2'
bmd: no visible global function definition for 'W2.2'
bmd: no visible global function definition for 'LL.5'
bmd: no visible global function definition for 'LN.4'
bmd: no visible global function definition for 'W1.4'
bmd: no visible global function definition for 'W2.4'
bmd: no visible global function definition for 'FPL.4'
bmd: no visible global function definition for 'maED'
bmd: no visible global function definition for 'ED'
Undefined global functions or variables:
  ED FPL.4 LL.2 LL.5 LN.2 LN.4 W1.2 W1.4 W2.2 W2.4 maED predict qnorm
Consider adding
  importFrom("stats", "predict", "qnorm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Amelia' 'MASS' 'lavaan' 'sem' 'snowfall'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  'coda' 'functional' 'plyr'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'coda' 'functional' 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HDistNoSize: no visible global function definition for 'density'
HDistSize: no visible global function definition for 'density'
bmkconverge: no visible global function definition for 'Compose'
bmksensitive: no visible global function definition for 'Compose'
bmksummary: no visible global function definition for 'Compose'
bmksummary: no visible global function definition for 'Curry'
bmksummary: no visible binding for global variable 'quantile'
bmksummary : std.error: no visible global function definition for 'var'
bmksummary: no visible global function definition for 'mcmc'
bmksummary: no visible global function definition for 'mcmc.list'
bmksummary: no visible global function definition for 'median'
bmksummary: no visible global function definition for 'effectiveSize'
bmksummary: no visible global function definition for 'gelman.diag'
Undefined global functions or variables:
  Compose Curry density effectiveSize gelman.diag mcmc mcmc.list median
  quantile var
Consider adding
  importFrom("stats", "density", "median", "quantile", "var")
to your NAMESPACE file.
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.
'::' or ':::' import not declared from: 'bnlearn'
'library' or 'require' call not declared from: 'mlbench'
make_topology: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
bnlr: no visible global function definition for 'dnorm'
bnlr: no visible global function definition for 'runif'
chainsum : <anonymous>: no visible global function definition for
  'quantile'
infocrit: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm quantile runif
Consider adding
  importFrom("stats", "dnorm", "quantile", "runif")
to your NAMESPACE file.
clusterplots: no visible global function definition for 'par'
clusterplots: no visible global function definition for 'rainbow'
clusterplots: no visible global function definition for 'plot'
clusterplots: no visible global function definition for 'axis'
clusterplots: no visible global function definition for 'lines'
diagplots: no visible global function definition for 'par'
diagplots: no visible global function definition for 'plot'
diagplots: no visible global function definition for 'hist'
tseriesca: no visible global function definition for 'rgamma'
tseriesca: no visible global function definition for 'runif'
tseriesca: no visible global function definition for 'dbeta'
tseriesca: no visible global function definition for 'dgamma'
tseriescm: no visible global function definition for 'rgamma'
tseriescm: no visible global function definition for 'runif'
tseriescm: no visible global function definition for 'dbeta'
tseriescm: no visible global function definition for 'dgamma'
tseriescq: no visible global function definition for 'rgamma'
tseriescq: no visible global function definition for 'runif'
tseriescq: no visible global function definition for 'dbeta'
tseriescq: no visible global function definition for 'dgamma'
Undefined global functions or variables:
  axis dbeta dgamma hist lines par plot rainbow rgamma runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "hist", "lines", "par", "plot")
  importFrom("stats", "dbeta", "dgamma", "rgamma", "runif")
to your NAMESPACE file.
BOGest: no visible global function definition for 'read.table'
BOGstat: no visible global function definition for 'phyper'
BOGstat: no visible global function definition for 'wilcox.test'
BOGstat: no visible global function definition for 'p.adjust'
gseaplot: no visible global function definition for 'par'
gseaplot: no visible global function definition for 'plot'
gseaplot: no visible global function definition for 'points'
gseaplot: no visible global function definition for 'axis'
gseaplot: no visible global function definition for 'segments'
hgplot: no visible global function definition for 'par'
hgplot: no visible global function definition for 'barplot'
Undefined global functions or variables:
  axis barplot p.adjust par phyper plot points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "plot", "points",
             "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/BonEV.Rcheck/00install.out' for details.
Found the following non-portable file paths:
  Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalGaussianRegressionAsisSampler.hpp
  Boom/inst/include/Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.hpp
  Boom/inst/include/Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.hpp

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
installed size is 79.9Mb
  sub-directories of 1Mb or more:
    include   3.0Mb
    lib      76.5Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
boostBackend: no visible global function definition for 'model.frame'
findFormulaIn: no visible global function definition for 'as.formula'
kFoldCV: no visible binding for global variable 'par'
predictResponseFromWeightedAverage: no visible global function
  definition for 'weighted.mean'
print.boostr: no visible global function definition for 'str'
Undefined global functions or variables:
  as.formula model.frame par str weighted.mean
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.formula", "model.frame", "weighted.mean")
  importFrom("utils", "str")
to your NAMESPACE file.
'library' or 'require' call to 'lpSolveAPI' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'genetics' 'lpSolveAPI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
alleleEnrichment: no visible binding for global variable 'na.omit'
alleleEnrichment: no visible binding for global variable 'na.pass'
alleleEnrichment: no visible global function definition for
  'write.table'
alleleEnrichment.data.alleles: no visible binding for global variable
  'na.omit'
alleleEnrichment.data.alleles: no visible binding for global variable
  'na.pass'
alleleEnrichment.data.alleles : <anonymous>: no visible global function
  definition for 'allele.count'
alleleEnrichment.data.alleles: no visible global function definition
  for 'runif'
alleleEnrichment.data.pheno: no visible global function definition for
  'read.table'
alleleEnrichment.lp: no visible global function definition for
  'make.lp'
alleleEnrichment.lp : <anonymous>: no visible global function
  definition for 'set.column'
alleleEnrichment.lp : <anonymous>: no visible global function
  definition for 'set.type'
alleleEnrichment.lp: no visible global function definition for
  'set.objfn'
alleleEnrichment.lp: no visible global function definition for
  'set.constr.type'
alleleEnrichment.lp: no visible global function definition for
  'set.rhs'
alleleEnrichment.lp: no visible global function definition for
  'lp.control'
alleleEnrichment.lp: no visible global function definition for
  'get.variables'
getGenotypes : <anonymous>: no visible global function definition for
  'genotype'
getRefAlleles: no visible global function definition for 'read.table'
getSnpWeights: no visible global function definition for 'read.table'
readMapfile: no visible global function definition for 'read.table'
Undefined global functions or variables:
  allele.count genotype get.variables lp.control make.lp na.omit
  na.pass read.table runif set.column set.constr.type set.objfn set.rhs
  set.type write.table
Consider adding
  importFrom("stats", "na.omit", "na.pass", "runif")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
specdens: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
boot.stepAIC: no visible global function definition for 'update'
boot.stepAIC: no visible binding for global variable 'coef'
boot.stepAIC : <anonymous>: no visible global function definition for
  'anova'
boot.stepAIC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  anova coef pnorm update
Consider adding
  importFrom("stats", "anova", "coef", "pnorm", "update")
to your NAMESPACE file.
bootSVD: no visible global function definition for 'object.size'
bootSVD : <anonymous> : <anonymous>: no visible global function
  definition for 'quantile'
bootSVD_LD: no visible global function definition for 'txtProgressBar'
bootSVD_LD: no visible global function definition for
  'setTxtProgressBar'
genQ: no visible global function definition for 'rnorm'
getHDpercentiles : <anonymous>: no visible global function definition
  for 'quantile'
getMomentsAndMomentCI: no visible binding for global variable 'var'
os: no visible global function definition for 'object.size'
simEEG: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  object.size quantile rnorm setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("stats", "quantile", "rnorm", "var")
  importFrom("utils", "object.size", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
boottol: no visible global function definition for 'setNames'
boottol : shift: no visible global function definition for 'tail'
boottol : shift: no visible global function definition for 'head'
boottol: no visible global function definition for 'na.omit'
vastol: no visible global function definition for 'setNames'
vastol: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  head na.omit setNames tail
Consider adding
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
bPeaksAnalysis: no visible global function definition for 'write.table'
dataReading: no visible global function definition for 'read.table'
dataSmoothing: no visible global function definition for 'filter'
peakDetection: no visible global function definition for 'quantile'
peakDetection: no visible global function definition for 'pdf'
peakDetection: no visible global function definition for 'par'
peakDetection: no visible global function definition for 'plot'
peakDetection: no visible global function definition for 'text'
peakDetection: no visible global function definition for 'abline'
peakDetection: no visible global function definition for 'points'
peakDetection: no visible global function definition for 'dev.off'
peakDetection: no visible global function definition for 'write.table'
peakDrawing: no visible global function definition for 'par'
peakDrawing: no visible global function definition for 'plot'
peakDrawing: no visible global function definition for 'abline'
peakLocation: no visible global function definition for 'read.table'
peakLocation: no visible global function definition for 'pdf'
peakLocation: no visible global function definition for 'barplot'
peakLocation: no visible global function definition for 'dev.off'
peakLocation: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline barplot dev.off filter par pdf plot points quantile read.table
  text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "plot", "points",
             "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
M0: no visible global function definition for 'fft'
M1: no visible global function definition for 'fft'
bpk: no visible binding for global variable 'dnorm'
bpkde: no visible binding for global variable 'dnorm'
bpkde: no visible binding for global variable 'bw.SJ'
bpkde: no visible global function definition for 'rnorm'
bpkde: no visible global function definition for 'fft'
bpkde: no visible global function definition for 'optimize'
contour.discretize.kernel: no visible global function definition for
  'contour.default'
contour.mvkde: no visible global function definition for
  'contour.default'
image.discretize.kernel: no visible global function definition for
  'image.default'
image.discretize.kernel: no visible global function definition for
  'gray'
image.mvkde: no visible global function definition for 'image.default'
image.mvkde: no visible global function definition for 'gray'
image.mvlinbin: no visible global function definition for 'image'
image.mvlinbin: no visible global function definition for 'gray'
plot.discretize.kernel: no visible global function definition for
  'mtext'
plot.discretize.kernel: no visible global function definition for 'par'
plot.mvkde: no visible global function definition for 'mtext'
plot.mvkde: no visible global function definition for 'par'
plot.mvlinbin: no visible global function definition for 'plot'
plot.mvlinbin: no visible global function definition for 'mtext'
plot.mvlinbin: no visible global function definition for 'par'
Undefined global functions or variables:
  bw.SJ contour.default dnorm fft gray image image.default mtext
  optimize par plot rnorm
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "contour.default", "image", "image.default",
             "mtext", "par", "plot")
  importFrom("stats", "bw.SJ", "dnorm", "fft", "optimize", "rnorm")
to your NAMESPACE file.
Package in Depends field not imported from: 'waveslim'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

const.cor.list: no visible global function definition for
  'wave.correlation'
const.var.list: no visible global function definition for
  'wave.variance'
fitting: no visible global function definition for 'hist'
fitting: no visible global function definition for 'nlm'
fitting: no visible global function definition for 'write.table'
p.value.compute: no visible global function definition for 'pnorm'
p.value.compute: no visible global function definition for 'pt'
random.attack: no visible global function definition for 'runif'
read.convert_1_2: no visible global function definition for
  'read.table'
read.cor.txt: no visible global function definition for 'read.table'
read.var.txt: no visible global function definition for 'read.table'
save.cor.txt: no visible global function definition for 'write.table'
save.var.txt: no visible global function definition for 'write.table'
sim.equadist: no visible global function definition for 'write.table'
small.world: no visible global function definition for 'dist'
small.world: no visible global function definition for 'write.table'
wave.trans: no visible global function definition for 'dwt'
wave.trans: no visible global function definition for 'modwt'
wave.trans: no visible global function definition for 'brick.wall'
Undefined global functions or variables:
  brick.wall dist dwt hist modwt nlm pnorm pt read.table runif
  wave.correlation wave.variance write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dist", "nlm", "pnorm", "pt", "runif")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
apply.breaks: no visible binding for global variable 'median'
break.clust: no visible global function definition for 'plot'
break.clust: no visible global function definition for 'median'
breakage.plot: no visible binding for global variable 'median'
breakage.plot: no visible global function definition for 'plot'
breakage.plot: no visible global function definition for 'abline'
breakage.plot: no visible global function definition for 'lm'
find.bottom: no visible global function definition for 'filter'
fit.breakage: no visible global function definition for 'optim'
fit.breakage: no visible global function definition for 'plot'
fit.breakage: no visible global function definition for 'points'
fit.sensitivity.plot: no visible global function definition for
  'contour'
fit.sensitivity.plot: no visible global function definition for
  'points'
fit.sensitivity.plot: no visible global function definition for 'text'
Undefined global functions or variables:
  abline contour filter lm median optim plot points text
Consider adding
  importFrom("graphics", "abline", "contour", "plot", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
'::' or ':::' import not declared from: 'gamlss.dist'
'library' or 'require' call not declared from: 'quantreg'
'data(package=)' call not declared from: 'gamlss.data'
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
BSGS.Sample: no visible global function definition for 'rgamma'
BSGS.Simple: no visible global function definition for 'rgamma'
CompWiseGibbs: no visible global function definition for 'runif'
CompWiseGibbs: no visible global function definition for 'rnorm'
CompWiseGibbsSMP: no visible global function definition for 'rbinom'
CompWiseGibbsSMP: no visible global function definition for 'runif'
CompWiseGibbsSMP: no visible global function definition for 'rnorm'
CompWiseGibbsSimple: no visible global function definition for 'runif'
CompWiseGibbsSimple: no visible global function definition for 'rnorm'
CompWiseGibbsSimple: no visible global function definition for 'rgamma'
GroupMH: no visible global function definition for 'runif'
GroupZ.MH: no visible global function definition for 'runif'
Undefined global functions or variables:
  rbinom rgamma rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rnorm", "runif")
to your NAMESPACE file.
plot.bspec: no visible global function definition for 'par'
plot.bspec: no visible global function definition for 'plot'
plot.bspec: no visible global function definition for 'matlines'
plot.bspec: no visible global function definition for 'points'
plot.bspec: no visible global function definition for 'axis'
plot.bspec: no visible global function definition for 'mtext'
plot.bspec: no visible global function definition for 'axTicks'
plot.bspec: no visible global function definition for 'box'
plot.bspecACF: no visible global function definition for 'plot'
plot.bspecACF: no visible global function definition for 'abline'
plot.bspecACF: no visible global function definition for 'matlines'
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par plot points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "plot", "points")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'VGAM' 'quadprog' 'quantreg'
  Please remove these calls from your code.
dqreg: no visible binding for global variable 'median'
dqreg: no visible global function definition for 'median'
log_pdf : q0: no visible global function definition for 'qnorm'
log_pdf : d0: no visible global function definition for 'dnorm'
log_pdf : q0: no visible global function definition for 'qt'
log_pdf : d0: no visible global function definition for 'dt'
log_pdf : q0: no visible global function definition for 'qweibull'
log_pdf : d0: no visible global function definition for 'dweibull'
log_pdf : q0: no visible global function definition for 'qgamma'
log_pdf : d0: no visible global function definition for 'dgamma'
make.B: no visible global function definition for 'qnorm'
make.B: no visible global function definition for 'qweibull'
make.B: no visible global function definition for 'qgamma'
qr_plot: no visible global function definition for 'gray'
qr_plot: no visible binding for global variable 'quantile'
qr_plot: no visible global function definition for 'polygon'
qr_plot: no visible global function definition for 'lines'
qreg: no visible global function definition for 'sd'
qreg: no visible global function definition for 'lm'
qreg: no visible global function definition for 'var'
qreg_spline: no visible global function definition for 'rnorm'
qreg_spline: no visible global function definition for 'var'
qreg_spline: no visible binding for global variable 'quantile'
rootfind: no visible global function definition for 'runif'
Undefined global functions or variables:
  dgamma dnorm dt dweibull gray lines lm median polygon qgamma qnorm qt
  quantile qweibull rnorm runif sd var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "polygon")
  importFrom("stats", "dgamma", "dnorm", "dt", "dweibull", "lm",
             "median", "qgamma", "qnorm", "qt", "quantile", "qweibull",
             "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Found the following Makefile(s) without a final LF:
  src/Makevars
Some 'make' programs ignore lines not ending in LF.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'btergm'
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'btergm'
See 'd:/Rcompile/CRANpkg/local/3.6/btergm.Rcheck/00install.out' for details.
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
alpha.proxy: no visible global function definition for 'filled.contour'
alpha.proxy: no visible global function definition for 'axis'
alpha.proxy: no visible global function definition for 'contour'
factor.model.stat: no visible global function definition for 'quantile'
factor.model.stat: no visible global function definition for 'lsfit'
partial.rainbow: no visible binding for global variable 'rainbow'
var.shrink.eqcor: no visible global function definition for 'var'
var.shrink.eqcor: no visible global function definition for 'quantile'
var.shrink.eqcor: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  axis contour cov2cor filled.contour lsfit quantile rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "contour", "filled.contour")
  importFrom("stats", "cov2cor", "lsfit", "quantile", "var")
to your NAMESPACE file.
plot.bursts: no visible global function definition for 'plot'
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 plot
Consider adding
  importFrom("graphics", "arrows", "axis", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'haplo.stats' 'msm'
  Please remove these calls from your code.
fitBVS: no visible global function definition for 'qnorm'
fitBVS: no visible global function definition for 'model.matrix'
fitBVS: no visible global function definition for 'as.formula'
fitBVS: no visible global function definition for 'glm'
fitBVS: no visible global function definition for 'deviance'
fitBVS: no visible global function definition for 'pnorm'
plotBVS: no visible global function definition for 'par'
plotBVS: no visible global function definition for 'image'
plotBVS: no visible global function definition for 'axis'
sampleBVS: no visible global function definition for 'qnorm'
sampleBVS: no visible global function definition for 'pnorm'
sampleBVS: no visible global function definition for 'runif'
summaryBVS: no visible global function definition for 'qnorm'
summaryBVS : inc.prob: no visible global function definition for
  'pnorm'
summaryBVS: no visible global function definition for 'pnorm'
summaryBVS: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  as.formula axis deviance glm image model.matrix par pnorm qnorm runif
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "as.formula", "deviance", "glm", "model.matrix",
             "pnorm", "qnorm", "runif")
to your NAMESPACE file.
makemim: no visible global function definition for 'cor'
sigtestMTC: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  cor p.adjust
Consider adding
  importFrom("stats", "cor", "p.adjust")
to your NAMESPACE file.
cabootcrs: no visible global function definition for 'read.table'
cabootcrs: no visible global function definition for 'rmultinom'
cabootcrs: no visible global function definition for 'rpois'
plotca : plotonepic: no visible global function definition for 'qchisq'
plotca : plotonepic: no visible global function definition for
  'dev.new'
plotca : plotonepic: no visible global function definition for 'plot'
plotca : plotonepic: no visible global function definition for 'points'
plotca : plotonepic: no visible global function definition for 'abline'
plotca : plotonepic: no visible global function definition for 'legend'
plotca : plotonepic: no visible global function definition for 'title'
plotca : plotonepic: no visible global function definition for 'lines'
plotca : plotonepic: no visible global function definition for 'text'
plotca: no visible global function definition for 'colours'
plotca: no visible global function definition for 'rainbow'
plotca: no visible global function definition for 'read.table'
Undefined global functions or variables:
  abline colours dev.new legend lines plot points qchisq rainbow
  read.table rmultinom rpois text title
Consider adding
  importFrom("grDevices", "colours", "dev.new", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "plot", "points",
             "text", "title")
  importFrom("stats", "qchisq", "rmultinom", "rpois")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'FastRWeb'
calibrate: no visible global function definition for 'lines'
calibrate: no visible global function definition for 'text'
canocor: no visible global function definition for 'cor'
circle: no visible global function definition for 'points'
dlines: no visible global function definition for 'lines'
origin: no visible global function definition for 'par'
origin: no visible global function definition for 'lines'
rda: no visible global function definition for 'cor'
rda: no visible global function definition for 'princomp'
rda: no visible global function definition for 'var'
textxy: no visible global function definition for 'text'
Undefined global functions or variables:
  cor lines par points princomp text var
Consider adding
  importFrom("graphics", "lines", "par", "points", "text")
  importFrom("stats", "cor", "princomp", "var")
to your NAMESPACE file.
EK.eqn10.supp: no visible global function definition for 'integrate'
MH: no visible global function definition for 'rmvnorm'
MH: no visible global function definition for 'runif'
computer.model: no visible global function definition for 'rmvnorm'
create.new.toy.datasets: no visible global function definition for
  'rnorm'
model.inadequacy: no visible global function definition for 'rmvnorm'
prob.psi1: no visible global function definition for 'dmvnorm'
prob.psi2: no visible global function definition for 'dmvnorm'
prob.theta: no visible global function definition for 'dmvnorm'
sample.theta: no visible global function definition for 'rmvnorm'
stage1: no visible global function definition for 'optim'
stage2: no visible global function definition for 'optim'
stage3: no visible global function definition for 'optim'
Undefined global functions or variables:
  dmvnorm integrate optim rmvnorm rnorm runif
Consider adding
  importFrom("stats", "integrate", "optim", "rnorm", "runif")
to your NAMESPACE file.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.6Mb
CAM: no visible global function definition for 'object.size'
CAM: no visible global function definition for 'as'
computeScoreMat: no visible global function definition for 'combn'
computeScoreMat: no visible global function definition for 'var'
computeScoreMatParallel: no visible global function definition for
  'var'
selLm: no visible global function definition for 'lm'
selLm: no visible global function definition for 'coef'
train_gam: no visible global function definition for 'formula'
train_lasso: no visible global function definition for 'predict'
train_linear: no visible global function definition for 'lm'
Undefined global functions or variables:
  as coef combn formula lm object.size predict var
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coef", "formula", "lm", "predict", "var")
  importFrom("utils", "combn", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in 'CANSIM2R-Ex.R' failed
The error most likely occurred in:

> ### Name: getCANSIM
> ### Title: getCANSIM
> ### Aliases: getCANSIM
> 
> ### ** Examples
> 
> getCANSIM(4010004, showLabels = FALSE)
Warning in download.file(url, temp, quiet = TRUE) :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in download.file(url, temp, quiet = TRUE) : 
  cannot open URL 'http://www20.statcan.gc.ca/tables-tableaux/cansim/csv/04010004-eng.zip'
Calls: getCANSIM -> downloadCANSIM -> download.file
Execution halted
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.
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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
abundance: no visible global function definition for 'D'
Undefined global functions or variables:
  D
Consider adding
  importFrom("stats", "D")
to your NAMESPACE file.
barplotEQR: no visible global function definition for 'barplot'
barplotEQR: no visible global function definition for 'abline'
barplotEQR: no visible global function definition for 'par'
barplotEQR: no visible global function definition for 'text'
Undefined global functions or variables:
  abline barplot par text
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "text")
to your NAMESPACE file.
'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.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.8Mb
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.
colAUC: no visible global function definition for 'plot'
colAUC: no visible global function definition for 'title'
colAUC: no visible global function definition for 'abline'
colAUC: no visible global function definition for 'legend'
colAUC: no visible global function definition for 'lines'
read.ENVI: no visible global function definition for 'read.table'
read.gif: no visible global function definition for 'download.file'
read.gif: no visible global function definition for 'rgb'
runmad: no visible global function definition for 'runmed'
runmad: no visible binding for global variable 'mad'
runquantile: no visible binding for global variable 'quantile'
runsd: no visible binding for global variable 'sd'
sample.split: no visible global function definition for 'runif'
write.gif: no visible global function definition for 'gray'
write.gif: no visible global function definition for 'colorRampPalette'
write.gif: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  abline col2rgb colorRampPalette download.file gray legend lines mad
  plot quantile read.table rgb runif runmed sd title
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "gray", "rgb")
  importFrom("graphics", "abline", "legend", "lines", "plot", "title")
  importFrom("stats", "mad", "quantile", "runif", "runmed", "sd")
  importFrom("utils", "download.file", "read.table")
to your NAMESPACE file.
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.
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.
binParamPosteriorSampling: no visible global function definition for
  'rbeta'
bindagMonteCarloCausalEffect: no visible global function definition for
  'runif'
getBinDAGModelData: no visible global function definition for 'runif'
logitDist: no visible global function definition for 'runif'
logitDist: no visible global function definition for 'rnorm'
simulateWitnessModel: no visible global function definition for 'runif'
summary.covsearch: no visible global function definition for 'quantile'
summary.iv: no visible global function definition for 'quantile'
summary.wpp: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile rbeta rnorm runif
Consider adding
  importFrom("stats", "quantile", "rbeta", "rnorm", "runif")
to your NAMESPACE file.
BinaryCut: no visible global function definition for 'quantile'
CleanNaFromContinuousFunction: no visible global function definition
  for 'median'
CleanNaFromContinuousFunction: no visible global function definition
  for 'na.omit'
GetMetadata.Connect: no visible global function definition for
  'dbGetQuery'
GetRawData.Connect: no visible global function definition for
  'dbGetQuery'
Linearity: no visible global function definition for 'median'
PredictivePowerCv: no visible global function definition for 'sd'
ReadCausataCsv: no visible global function definition for 'read.csv'
ToPmml.GlmnetModelDefinition: no visible global function definition for
  'coef'
ToPmml.GlmnetModelDefinition: no visible global function definition for
  'terms.formula'
ValidateModel: no visible global function definition for 'predict'
predict.GlmnetModelDefinition: no visible global function definition
  for 'model.matrix'
predict.GlmnetModelDefinition: no visible binding for global variable
  'contrasts'
predict.GlmnetModelDefinition: no visible global function definition
  for 'predict'
Undefined global functions or variables:
  coef contrasts dbGetQuery median model.matrix na.omit predict
  quantile read.csv sd terms.formula
Consider adding
  importFrom("stats", "coef", "contrasts", "median", "model.matrix",
             "na.omit", "predict", "quantile", "sd", "terms.formula")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for 'cor'
img.estim.regul: no visible global function definition for 'par'
img.estim.regul: no visible global function definition for 'image'
img.estim.regul: no visible global function definition for
  'heat.colors'
img.estim.regul: no visible global function definition for 'axis'
img.estim.regul: no visible global function definition for 'box'
img.matcor: no visible global function definition for 'par'
img.matcor: no visible global function definition for 'image'
img.matcor: no visible global function definition for 'box'
img.matcor: no visible global function definition for 'abline'
img.matcor: no visible global function definition for 'layout'
loo: no visible global function definition for 'cor'
matcor: no visible global function definition for 'cor'
plt.cc: no visible global function definition for 'par'
plt.cc: no visible global function definition for 'layout'
plt.indiv: no visible global function definition for 'plot'
plt.indiv: no visible global function definition for 'text'
plt.indiv: no visible global function definition for 'abline'
plt.var: no visible global function definition for 'plot'
plt.var: no visible global function definition for 'points'
plt.var: no visible global function definition for 'text'
plt.var: no visible global function definition for 'abline'
plt.var: no visible global function definition for 'lines'
rcc: no visible global function definition for 'var'
rcc: no visible global function definition for 'cov'
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
ccd.sequential: no visible global function definition for 'qchisq'
dominate.random.sample: no visible global function definition for
  'runif'
draw.circle: no visible global function definition for 'polygon'
juggle2: no visible global function definition for 'rbinom'
plot.cccd: no visible global function definition for 'gray'
plot.cccd: no visible global function definition for 'plot'
plot.cccd: no visible global function definition for 'points'
plot.cccdClassifier: no visible global function definition for 'points'
plot.cccdClassifier: no visible global function definition for 'plot'
plot.ccd: no visible global function definition for 'plot'
Undefined global functions or variables:
  gray plot points polygon qchisq rbinom runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot", "points", "polygon")
  importFrom("stats", "qchisq", "rbinom", "runif")
to your NAMESPACE file.
VD: no visible binding for global variable 'var'
stratcc : <anonymous>: no visible global function definition for
  'hclust'
stratcc : <anonymous>: no visible global function definition for
  'cutree'
Undefined global functions or variables:
  cutree hclust var
Consider adding
  importFrom("stats", "cutree", "hclust", "var")
to your NAMESPACE file.
ccda.main: no visible global function definition for 'hclust'
ccda.main: no visible global function definition for 'dist'
ccda.main: no visible global function definition for 'cutree'
ccda.main: no visible global function definition for 'quantile'
percentage: no visible global function definition for 'predict'
plotccda.cluster: no visible global function definition for 'par'
plotccda.cluster: no visible global function definition for 'plot'
plotccda.q95: no visible global function definition for 'par'
plotccda.q95: no visible global function definition for 'plot'
plotccda.q95: no visible global function definition for 'density'
plotccda.q95: no visible global function definition for 'abline'
plotccda.q95: no visible global function definition for 'legend'
plotccda.q95: no visible global function definition for 'strwidth'
plotccda.q95: no visible global function definition for 'strheight'
plotccda.results: no visible global function definition for 'par'
plotccda.results: no visible global function definition for 'plot'
plotccda.results: no visible global function definition for 'axis'
plotccda.results: no visible global function definition for 'lines'
plotccda.results: no visible global function definition for 'legend'
plotccda.results: no visible global function definition for 'strwidth'
plotccda.results: no visible global function definition for 'strheight'
Undefined global functions or variables:
  abline axis cutree density dist hclust legend lines par plot predict
  quantile strheight strwidth
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "strheight", "strwidth")
  importFrom("stats", "cutree", "density", "dist", "hclust", "predict",
             "quantile")
to your NAMESPACE file.
dcc.est: no visible global function definition for 'cov'
dcc.estimation1: no visible global function definition for 'optim'
dcc.estimation2: no visible global function definition for
  'constrOptim'
dlc: no visible global function definition for 'cov'
eccc.estimation: no visible global function definition for 'optim'
hh.test : uni.garch : uni.garch.est : garch.ll: no visible global
  function definition for 'dnorm'
hh.test : uni.garch : uni.garch.est: no visible global function
  definition for 'optim'
hh.test: no visible global function definition for 'lm'
hh.test: no visible global function definition for 'pchisq'
jb.test: no visible global function definition for 'pchisq'
ljung.box.test: no visible global function definition for 'pchisq'
nt.test : uni.garch : uni.garch.est : garch.ll: no visible global
  function definition for 'dnorm'
nt.test : uni.garch : uni.garch.est: no visible global function
  definition for 'optim'
nt.test: no visible global function definition for 'lm'
nt.test: no visible global function definition for 'pchisq'
rob.kr: no visible global function definition for 'quantile'
rob.sk: no visible global function definition for 'quantile'
Undefined global functions or variables:
  constrOptim cov dnorm lm optim pchisq quantile
Consider adding
  importFrom("stats", "constrOptim", "cov", "dnorm", "lm", "optim",
             "pchisq", "quantile")
to your NAMESPACE file.
p.Roy: no visible global function definition for 'pf'
p.asym: no visible global function definition for 'pf'
p.perm: no visible global function definition for 'cancor'
plt.asym: no visible global function definition for 'qf'
plt.asym: no visible global function definition for 'plot'
plt.asym: no visible global function definition for 'df'
plt.asym: no visible global function definition for 'abline'
plt.perm: no visible global function definition for 'hist'
plt.perm: no visible global function definition for 'mtext'
plt.perm: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline cancor df hist mtext pf plot qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext", "plot")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
'library' or 'require' call to 'bitops' which was already attached by Depends.
  Please remove these calls from your code.
bw: no visible global function definition for 'optimize'
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
CDFt: no visible global function definition for 'ecdf'
CDFt: no visible global function definition for 'quantile'
CDFt: no visible global function definition for 'approx'
KolmogorovSmirnov: no visible global function definition for 'ecdf'
KolmogorovSmirnov: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx ecdf quantile
Consider adding
  importFrom("stats", "approx", "ecdf", "quantile")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
Packages in Depends field not imported from:
  'gplots' 'minpack.lm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
erf: no visible global function definition for 'pnorm'
fitVolDist: no visible global function definition for 'nls.lm'
fitVolDist: no visible global function definition for 'nls.lm.control'
fitVolDist: no visible global function definition for 'optim'
fitVolDist: no visible global function definition for 'relist'
print.fitVolDist: no visible global function definition for 'coef'
print.fitVolDist: no visible global function definition for 'deviance'
print.fitVolDist: no visible global function definition for 'pt'
print.fitVolDist: no visible global function definition for
  'printCoefmat'
resFunChiSq: no visible global function definition for 'relist'
volEq7: no visible global function definition for 'integrate'
Undefined global functions or variables:
  coef deviance integrate nls.lm nls.lm.control optim pnorm
  printCoefmat pt relist
Consider adding
  importFrom("stats", "coef", "deviance", "integrate", "optim", "pnorm",
             "printCoefmat", "pt")
  importFrom("utils", "relist")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.0Mb
cenNID: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
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.
CM: no visible global function definition for 'sd'
Erf: no visible global function definition for 'pnorm'
Erfc: no visible global function definition for 'pnorm'
boot.Cenarma: no visible global function definition for 'coef'
boot.Cenarma: no visible global function definition for 'arima.sim'
cenarma: no visible global function definition for 'arima'
cenarma: no visible global function definition for 'coef'
cenarma: no visible global function definition for 'ARMAacf'
cenarma: no visible global function definition for 'var'
plot.cents: no visible global function definition for 'plot'
plot.cents: no visible global function definition for 'segments'
plot.cents: no visible global function definition for 'rgb'
plot.cents: no visible global function definition for 'points'
rcarma: no visible global function definition for 'arima.sim'
rcarma: no visible global function definition for 'quantile'
scenNID: no visible global function definition for 'sd'
se.Cenarma: no visible global function definition for 'coef'
se.Cenarma: no visible global function definition for 'sd'
Undefined global functions or variables:
  ARMAacf arima arima.sim coef plot pnorm points quantile rgb sd
  segments var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "ARMAacf", "arima", "arima.sim", "coef", "pnorm",
             "quantile", "sd", "var")
to your NAMESPACE file.
select_lambda: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
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.
sw.plot : <anonymous>: no visible global function definition for
  'median'
sw.plot : <anonymous>: no visible global function definition for 'mad'
sw.plot : my.line: no visible global function definition for 'lines'
sw.plot : island.line: no visible global function definition for
  'lines'
sw.plot: no visible global function definition for 'plot'
sw.plot: no visible global function definition for 'rug'
sw.plot: no visible global function definition for 'axis'
sw.plot: no visible global function definition for 'mtext'
sw.plot: no visible global function definition for 'abline'
sw.plot: no visible global function definition for 'points'
sw.rob : <anonymous>: no visible global function definition for
  'median'
sw.rob : <anonymous>: no visible global function definition for 'mad'
sw.threshold : <anonymous>: no visible global function definition for
  'median'
sw.threshold : <anonymous>: no visible global function definition for
  'mad'
Undefined global functions or variables:
  abline axis lines mad median mtext plot points rug
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "plot",
             "points", "rug")
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
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.
'library' or 'require' call to 'RCurl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RCurl' 'bitops' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createDataset: no visible global function definition for 'read.csv'
createInventory: no visible global function definition for 'read.csv'
downloadMaster: no visible global function definition for
  'getURLContent'
downloadMaster: no visible global function definition for 'read.csv'
downloadMaster: no visible global function definition for 'write.csv'
getMissingScrape: no visible global function definition for 'read.csv'
readLocalMaster: no visible global function definition for 'read.csv'
readMonthlyCsv: no visible global function definition for 'read.csv'
scrapeToCsv: no visible global function definition for 'download.file'
writeData: no visible global function definition for 'write.csv'
writeGhcn: no visible global function definition for 'write.table'
writeInventory: no visible global function definition for 'write.table'
writeMonthlyStations: no visible global function definition for
  'read.csv'
writeMonthlyStations: no visible global function definition for
  'write.csv'
Undefined global functions or variables:
  download.file getURLContent read.csv write.csv write.table
Consider adding
  importFrom("utils", "download.file", "read.csv", "write.csv",
             "write.table")
to your NAMESPACE file.
Running 'test-all.R' [26s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(cli)
  > library(testthat)
  > old.env <- Sys.getenv("checkpoint.mock.install")
  > Sys.setenv("checkpoint.mock.install" = TRUE)
  > test_check("checkpoint")
  Loading required package: checkpoint
  
  checkpoint: Part of the Reproducible R Toolkit from Microsoft
  https://mran.microsoft.com/documents/rro/reproducibility/
  -- 1. Failure: is.404 (@test-0-is-404.R#11)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot") isn't false.
  
  -- 2. Failure: is.404 (@test-0-is-404.R#14)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot/2015-05-01") isn't false.
  
  == testthat results  ===========================================================
  OK: 60 SKIPPED: 7 FAILED: 2
  1. Failure: is.404 (@test-0-is-404.R#11) 
  2. Failure: is.404 (@test-0-is-404.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   2.5Mb
choicemodelr : drawDelta: no visible global function definition for
  'rnorm'
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for 'rnorm'
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for 'runif'
choicemodelr : rmultireg: no visible global function definition for
  'rnorm'
choicemodelr : rwishart: no visible global function definition for
  'rchisq'
choicemodelr : rwishart: no visible global function definition for
  'rnorm'
choicemodelr : fsh: no visible global function definition for
  'flush.console'
choicemodelr: no visible global function definition for 'matplot'
choicemodelr: no visible global function definition for 'write.table'
Undefined global functions or variables:
  flush.console matplot rchisq rnorm runif write.table
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "rchisq", "rnorm", "runif")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
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.
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.
combineToSingleMatrix: no visible global function definition for
  'read.table'
combineToSingleMatrix: no visible global function definition for
  'write.table'
compareCIM: no visible global function definition for 'sd'
correctData: no visible global function definition for 'wd'
correctData: no visible global function definition for 'threshold'
correctData: no visible binding for global variable 'madmad'
correctData: no visible global function definition for 'wr'
Undefined global functions or variables:
  madmad read.table sd threshold wd wr write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
cin: no visible global function definition for 'pnorm'
gammaHRF: no visible global function definition for 'dgamma'
intertest: no visible global function definition for 'pnorm'
truncSum: no visible global function definition for 'spline'
Undefined global functions or variables:
  dgamma pnorm spline
Consider adding
  importFrom("stats", "dgamma", "pnorm", "spline")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.6/CircStats.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'boot'
  Please remove these calls from your code.
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.
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 'plot'
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 plot read.table rect screen split.screen tail
  text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 401-417 (cjamp.Rmd) 
Error: processing vignette 'cjamp.Rmd' failed with diagnostics:
need finite 'xlim' values
Execution halted
areas_list_to_states_list_old: no visible global function definition
  for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
'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.
classify.bug: no visible global function definition for
  'txtProgressBar'
classify.bug: no visible global function definition for
  'setTxtProgressBar'
plot.scores: no visible binding for global variable 'quantile'
plot.scores: no visible global function definition for 'runif'
plot.scores: no visible binding for global variable 'median'
scores.gpcm.bug: no visible global function definition for
  'txtProgressBar'
scores.gpcm.bug: no visible global function definition for
  'setTxtProgressBar'
across.reps,classification: no visible global function definition for
  'sd'
Undefined global functions or variables:
  median quantile runif sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "median", "quantile", "runif", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
.boxRadial: no visible global function definition for 'predict'
.radialSVM: no visible global function definition for 'predict'
cfPredict: no visible global function definition for 'predict'
getPerm5Num: no visible global function definition for 'median'
getPerm5Num: no visible global function definition for 'quantile'
ggClassPred: no visible global function definition for 'ftable'
ggEnsHist: no visible global function definition for 'sd'
ggPermHist: no visible global function definition for 'sd'
Undefined global functions or variables:
  ftable median predict quantile sd
Consider adding
  importFrom("stats", "ftable", "median", "predict", "quantile", "sd")
to your NAMESPACE file.
climdexInput.csv : get.and.check.data: no visible global function
  definition for 'read.csv'
get.prec.var.quantiles: no visible global function definition for
  'quantile'
growing.season.length : <anonymous>: no visible global function
  definition for 'head'
Undefined global functions or variables:
  head quantile read.csv
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "head", "read.csv")
to your NAMESPACE file.
clime: no visible global function definition for 'cov'
cv.clime: no visible global function definition for 'cov'
cv.clime: no visible binding for global variable 'sd'
Undefined global functions or variables:
  cov sd
Consider adding
  importFrom("stats", "cov", "sd")
to your NAMESPACE file.
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.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
socp: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to 'ggplot2' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'::' or ':::' import not declared from: 'tibble'
IGP.clusterRepro: no visible global function definition for 'cor'
permuteCol: no visible global function definition for 'runif'
Undefined global functions or variables:
  cor runif
Consider adding
  importFrom("stats", "cor", "runif")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
hopkins: no visible global function definition for 'runif'
hopkins: no visible global function definition for 'dist'
Undefined global functions or variables:
  dist runif
Consider adding
  importFrom("stats", "dist", "runif")
to your NAMESPACE file.
clustomit: no visible binding for global variable 'weighted.mean'
sim_unif : multivariate_unif: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif weighted.mean
Consider adding
  importFrom("stats", "runif", "weighted.mean")
to your NAMESPACE file.
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 suggested but not available for checking: 'moe430a.db'
'library' or 'require' calls in package code:
  'Biobase' 'GO.db' 'annotate' 'kohonen' 'mclust'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cma_es: no visible global function definition for 'rnorm'
f_rand: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
alpha.cronbach: no visible global function definition for 'cov'
alpha.curve: no visible global function definition for 'plot'
alpha.curve: no visible global function definition for 'text'
Undefined global functions or variables:
  cov plot text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
CMF: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
ComputeLambdaAndNuHat.shiftCMPest: no visible global function
  definition for 'nlminb'
ControlCharts: no visible global function definition for
  'com.log.density'
ControlCharts: no visible global function definition for 'plot'
ControlCharts: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline com.log.density nlminb plot
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "nlminb")
to your NAMESPACE file.
crr: no visible binding for global variable 'na.omit'
crr: no visible global function definition for 'approx'
cuminc: no visible binding for global variable 'na.omit'
cuminc: no visible global function definition for 'pchisq'
plot.cuminc: no visible global function definition for 'par'
plot.cuminc: no visible global function definition for 'plot'
plot.cuminc: no visible binding for global variable 'legend'
plot.cuminc: no visible global function definition for 'lines'
plot.predict.crr: no visible global function definition for 'plot'
plot.predict.crr: no visible global function definition for 'lines'
print.crr: no visible global function definition for 'pnorm'
summary.crr: no visible global function definition for 'pnorm'
summary.crr: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  approx legend lines na.omit par pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("stats", "approx", "na.omit", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
copynumberBootstrap: no visible global function definition for
  'txtProgressBar'
copynumberBootstrap: no visible global function definition for
  'quantile'
copynumberBootstrap: no visible global function definition for
  'setTxtProgressBar'
gethits: no visible global function definition for 'read.table'
normalizeGC: no visible global function definition for 'median'
plotCNOGpro: no visible global function definition for 'par'
plotCNOGpro: no visible global function definition for 'plot'
plotCNOGpro: no visible global function definition for 'rainbow'
plotCNOGpro: no visible global function definition for 'density'
plotCNOGpro: no visible global function definition for 'polygon'
plotCNOGpro: no visible global function definition for 'lines'
plotCNOGpro: no visible global function definition for 'legend'
plotCNOGpro: no visible global function definition for 'boxplot'
sampleChromosome: no visible global function definition for 'median'
sampleChromosome: no visible binding for global variable 'var'
setupEmissionMatrix: no visible global function definition for 'dgeom'
store: no visible global function definition for 'write.table'
Undefined global functions or variables:
  boxplot density dgeom legend lines median par plot polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "plot",
             "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
CNclusterNcenter: no visible global function definition for 'median'
CNclusterNcenter: no visible binding for global variable 'var'
breakIntoGaps: no visible global function definition for 'runif'
centerprob: no visible global function definition for 'pnorm'
getz: no visible global function definition for 'predict'
smad: no visible global function definition for 'mad'
smedian: no visible global function definition for 'median'
smedian.sample: no visible global function definition for 'median'
smedmad: no visible global function definition for 'median'
smedmad: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad median pnorm predict runif var
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "predict", "runif",
             "var")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data     3.5Mb
    exdata   5.5Mb
Running examples in 'coala-Ex.R' failed
The error most likely occurred in:

> ### Name: sumstat_sfs
> ### Title: Summary Statistic: Site Frequency Spectrum
> ### Aliases: sumstat_sfs
> 
> ### ** Examples
> 
> model <- coal_model(20, 500) +
+   feat_mutation(2) +
+   sumstat_sfs()
> stats <- simulate(model)
coalescentMCMC: no visible global function definition for
  'packageVersion'
coalescentMCMC : getparams: no visible global function definition for
  'nlminb'
sim.coalescent: no visible global function definition for 'plot'
sim.coalescent: no visible global function definition for 'segments'
sim.coalescent: no visible global function definition for 'points'
Undefined global functions or variables:
  nlminb packageVersion plot points segments
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
'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.
Package which this enhances but not available for checking: 'rkward'
Package in Depends field not imported from: 'coda'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BMDE: no visible global function definition for 'quantile'
BMDU: no visible global function definition for 'runif'
BMDU: no visible global function definition for 'quantile'
FS: no visible global function definition for 'qnorm'
GM: no visible global function definition for 'qchisq'
QH: no visible global function definition for 'qchisq'
SG : sgp: no visible global function definition for 'ppois'
SG : sgp: no visible global function definition for 'dpois'
WALD: no visible global function definition for 'qchisq'
WALDCC: no visible global function definition for 'qchisq'
WS: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  dpois ppois qchisq qnorm quantile runif
Consider adding
  importFrom("stats", "dpois", "ppois", "qchisq", "qnorm", "quantile",
             "runif")
to your NAMESPACE file.
'library' or 'require' call not declared from: 'tibble'
cICA: no visible global function definition for 'mvfft'
cICA: no visible global function definition for 'ar.yw'
cICA: no visible global function definition for 'rnorm'
scICA: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  ar.yw mvfft rnorm
Consider adding
  importFrom("stats", "ar.yw", "mvfft", "rnorm")
to your NAMESPACE file.
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.
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.
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.
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.
'library' or 'require' calls in package code:
  'lattice' 'rgl'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
showGuideForJavaGUIs: no visible global function definition for
  'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
p.Johansen: no visible global function definition for 'pgamma'
plotComT: no visible global function definition for 'axis'
plotComT: no visible global function definition for 'title'
plotComT: no visible global function definition for 'lines'
plotComT: no visible global function definition for 'box'
q.Johansen: no visible global function definition for 'qgamma'
Undefined global functions or variables:
  axis box lines pgamma qgamma title
Consider adding
  importFrom("graphics", "axis", "box", "lines", "title")
  importFrom("stats", "pgamma", "qgamma")
to your NAMESPACE file.
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 'plot'
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 plot
Consider adding
  importFrom("graphics", "axis", "mtext", "par", "plot")
to your NAMESPACE file.
compareC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to 'XML' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
compareODM: no visible global function definition for 'xmlRoot'
compareODM: no visible global function definition for 'xmlTreeParse'
compareODM: no visible global function definition for 'xmlChildren'
compareODM: no visible global function definition for 'xmlAttrs'
compareODM: no visible global function definition for 'xmlValue'
Undefined global functions or variables:
  xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue
two.level.comparison.items: no visible global function definition for
  'complete.cases'
two.level.components: no visible global function definition for
  'complete.cases'
plot,ece: no visible global function definition for 'par'
plot,ece: no visible global function definition for 'points'
plot,ece: no visible global function definition for 'mtext'
plot,ece: no visible global function definition for 'legend'
plot,ece: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline complete.cases legend mtext par points
Consider adding
  importFrom("graphics", "abline", "legend", "mtext", "par", "points")
  importFrom("stats", "complete.cases")
to your NAMESPACE file.
CIFplot: no visible global function definition for 'plot'
CIFplot: no visible global function definition for 'gray'
CIFplot: no visible global function definition for 'lines'
iprop: no visible global function definition for 'qnorm'
irates: no visible global function definition for 'qnorm'
irates.ratio: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  gray lines plot qnorm
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'inSilicoDb'
Package in Depends field not imported from: 'numDeriv'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dcomplnorm: no visible global function definition for 'grad'
dcomplnorm : f1: no visible global function definition for 'dlnorm'
dcomplnorm : F1: no visible global function definition for 'plnorm'
dcomplnorm : f1L: no visible global function definition for 'dlnorm'
dcomplnorm : F1L: no visible global function definition for 'plnorm'
pcomplnorm: no visible global function definition for 'grad'
pcomplnorm : f1: no visible global function definition for 'dlnorm'
pcomplnorm : F1: no visible global function definition for 'plnorm'
pcomplnorm : F1L: no visible global function definition for 'plnorm'
qcomplnorm: no visible global function definition for 'grad'
qcomplnorm : f1: no visible global function definition for 'dlnorm'
qcomplnorm : F1q: no visible global function definition for 'qlnorm'
qcomplnorm : F1: no visible global function definition for 'plnorm'
rcomplnorm: no visible global function definition for 'runif'
Undefined global functions or variables:
  dlnorm grad plnorm qlnorm runif
Consider adding
  importFrom("stats", "dlnorm", "plnorm", "qlnorm", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'hypergeo' which was already attached by Depends.
  Please remove these calls from your code.
momentCompound: no visible global function definition for 'integrate'
pgfIhypergeometric: no visible global function definition for 'uniroot'
pgfIhyperpoisson: no visible global function definition for 'uniroot'
pgfIkattitypeh1: no visible global function definition for 'uniroot'
pgfIkattitypeh2: no visible global function definition for 'uniroot'
pgfIneymantypeb: no visible global function definition for 'uniroot'
pgfIneymantypec: no visible global function definition for 'uniroot'
pgfIpoissonlindley: no visible global function definition for 'uniroot'
pgfIthomas: no visible global function definition for 'uniroot'
pgfIwaring: no visible global function definition for 'uniroot'
pgfIyule: no visible global function definition for 'uniroot'
rCompound: no visible global function definition for 'runif'
Undefined global functions or variables:
  integrate runif uniroot
Consider adding
  importFrom("stats", "integrate", "runif", "uniroot")
to your NAMESPACE file.
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.
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.
Package in Depends field not imported from: 'evd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
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 'plot'
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 'plot'
plotEllipsis: no visible global function definition for 'points'
plotHyperbola: no visible global function definition for 'lines'
plotHyperbola: no visible global function definition for 'plot'
plotHyperbola: no visible global function definition for 'points'
plotParabola: no visible global function definition for 'lines'
plotParabola: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline lines palette plot points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "plot", "points")
to your NAMESPACE file.
'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.
Conjoint: no visible global function definition for 'dev.new'
Conjoint: no visible global function definition for 'barplot'
caFactorialDesign: no visible global function definition for 'cor'
caModel: no visible global function definition for 'as.formula'
caModel: no visible global function definition for 'lm'
caModel: no visible global function definition for 'summary.lm'
caSegmentation: no visible global function definition for 'kmeans'
caUtilities: no visible global function definition for 'as.formula'
caUtilities: no visible global function definition for 'lm'
caUtilities: no visible global function definition for 'summary.lm'
partutilities: no visible global function definition for 'as.formula'
partutilities: no visible global function definition for 'lm'
partutils: no visible global function definition for 'as.formula'
partutils: no visible global function definition for 'lm'
profsimcode: no visible global function definition for 'as.formula'
profsimcode: no visible global function definition for 'lm'
profsimcode: no visible global function definition for 'model.matrix'
totalutilities: no visible global function definition for 'as.formula'
totalutilities: no visible global function definition for 'lm'
totalutilities: no visible global function definition for
  'model.matrix'
utlsplot: no visible global function definition for 'dev.new'
utlsplot: no visible global function definition for 'barplot'
Undefined global functions or variables:
  as.formula barplot cor dev.new kmeans lm model.matrix summary.lm
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "barplot")
  importFrom("stats", "as.formula", "cor", "kmeans", "lm",
             "model.matrix", "summary.lm")
to your NAMESPACE file.
maCooperative: no visible global function definition for 'points'
maCooperative: no visible global function definition for 'legend'
maPessimistic: no visible global function definition for 'combn'
maRules: no visible global function definition for 'capture.output'
mstCooperative: no visible global function definition for 'points'
mstCooperative: no visible global function definition for 'legend'
mstOptimistic: no visible global function definition for 'combn'
mstPessimistic: no visible global function definition for 'combn'
mstRules: no visible global function definition for 'capture.output'
plotCoreSet: no visible global function definition for 'points'
plotCoreSet: no visible global function definition for 'polygon'
plotImputationSet: no visible global function definition for 'par'
plotImputationSet: no visible global function definition for 'plot'
plotImputationSet: no visible global function definition for 'box'
plotImputationSet: no visible global function definition for 'polygon'
plotImputationSet: no visible global function definition for 'text'
shapleyValue: no visible global function definition for 'combn'
Undefined global functions or variables:
  box capture.output combn legend par plot points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "plot", "points",
             "polygon", "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
density_conditional: no visible global function definition for 'ppois'
density_joint: no visible global function definition for 'ppois'
dgam: no visible global function definition for 'dgamma'
dpolicy_loss: no visible global function definition for 'ppois'
dztp: no visible global function definition for 'dpois'
epolicy_loss: no visible global function definition for 'integrate'
mle_joint: no visible global function definition for 'optim'
mle_marginal: no visible global function definition for 'glm'
mle_marginal: no visible global function definition for 'Gamma'
mle_marginal: no visible global function definition for 'vcov'
mle_marginal: no visible global function definition for 'poisson'
mle_marginal: no visible global function definition for 'coef'
mle_marginal: no visible global function definition for 'ppois'
mle_marginal: no visible global function definition for 'optim'
pgam: no visible global function definition for 'pgamma'
ppolicy_loss: no visible global function definition for 'integrate'
pztp: no visible global function definition for 'ppois'
qpolicy_loss: no visible global function definition for 'uniroot'
rgam: no visible global function definition for 'rgamma'
vuongtest: no visible global function definition for 'sd'
ztp.glm: no visible global function definition for 'coef'
ztp.glm: no visible global function definition for 'glm'
ztp.glm: no visible binding for global variable 'poisson'
ztp.glm: no visible global function definition for 'optim'
Undefined global functions or variables:
  Gamma coef dgamma dpois glm integrate optim pgamma poisson ppois
  rgamma sd uniroot vcov
Consider adding
  importFrom("stats", "Gamma", "coef", "dgamma", "dpois", "glm",
             "integrate", "optim", "pgamma", "poisson", "ppois",
             "rgamma", "sd", "uniroot", "vcov")
to your NAMESPACE file.
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.
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.
compute.llh: no visible global function definition for 'dnorm'
compute.u.hat.simple: no visible global function definition for 'dnorm'
fit.CLM.1u.simple.start: no visible global function definition for
  'kmeans'
fit.CLMM.simple.start: no visible global function definition for
  'kmeans'
fit.CLMM.simple.start.NA: no visible global function definition for
  'kmeans'
Undefined global functions or variables:
  dnorm kmeans
Consider adding
  importFrom("stats", "dnorm", "kmeans")
to your NAMESPACE file.
binom.pval: no visible global function definition for 'pbinom'
chisq.pval: no visible global function definition for 'pchisq'
chisq.pval: no visible global function definition for 'pnorm'
fisher.pval: no visible global function definition for 'phyper'
prop.cint: no visible global function definition for 'qbeta'
prop.cint: no visible global function definition for 'qnorm'
sample.df: no visible global function definition for 'is'
simulated.census: no visible global function definition for 'runif'
simulated.census : height2weight: no visible global function definition
  for 'rnorm'
simulated.census : height2shoe: no visible global function definition
  for 'rnorm'
simulated.census: no visible global function definition for 'rnorm'
simulated.wikipedia: no visible global function definition for 'runif'
simulated.wikipedia: no visible global function definition for 'rnorm'
z.score.pval: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  is pbinom pchisq phyper pnorm qbeta qnorm rnorm runif
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "pbinom", "pchisq", "phyper", "pnorm", "qbeta",
             "qnorm", "rnorm", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
CBData: no visible global function definition for 'aggregate'
CMData: no visible global function definition for 'aggregate'
GEE.trend.test: no visible binding for global variable 'binomial'
GEE.trend.test: no visible global function definition for 'pnorm'
RS.trend.test: no visible global function definition for 'pnorm'
SO.mc.est: no visible global function definition for 'xtabs'
SO.trend.test : boot.LRT.fun: no visible global function definition for
  'aggregate'
jointprobs: no visible global function definition for 'xtabs'
mc.test.chisq.CBData: no visible global function definition for
  'pchisq'
mc.test.chisq.CMData : get.T: no visible global function definition for
  'weighted.mean'
mc.test.chisq.CMData: no visible global function definition for
  'pchisq'
mg.DirMult : <anonymous>: no visible global function definition for
  'rmultinom'
mg.LogitNorm : <anonymous>: no visible global function definition for
  'rmultinom'
mg.MixMult : <anonymous>: no visible global function definition for
  'rmultinom'
mg.Resample: no visible global function definition for 'rmultinom'
ran.CBData : ran.gen: no visible global function definition for
  'rmultinom'
read.CBData: no visible global function definition for 'read.table'
read.CBData: no visible global function definition for 'aggregate'
read.CMData: no visible global function definition for 'read.table'
trend.test : boot.LRT.fun: no visible global function definition for
  'aggregate'
unwrap.CMData: no visible global function definition for 'reshape'
Undefined global functions or variables:
  aggregate binomial pchisq pnorm read.table reshape rmultinom
  weighted.mean xtabs
Consider adding
  importFrom("stats", "aggregate", "binomial", "pchisq", "pnorm",
             "reshape", "rmultinom", "weighted.mean", "xtabs")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package suggested but not available for checking: 'ProData'
Package in Depends field not imported from: 'calibrate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
correlogram: no visible global function definition for 'par'
correlogram: no visible global function definition for 'plot'
correlogram: no visible global function definition for 'points'
correlogram: no visible global function definition for 'textxy'
correlogram: no visible global function definition for 'arrows'
correlogram: no visible global function definition for 'circle'
fit_angles: no visible global function definition for 'runif'
fit_angles: no visible global function definition for 'nlminb'
linangplot: no visible global function definition for 'cor'
linangplot: no visible global function definition for 'rad2degree'
linangplot: no visible global function definition for 'ginv'
linangplot: no visible global function definition for 'par'
linangplot: no visible global function definition for 'plot'
linangplot: no visible global function definition for 'calibrate'
linangplot: no visible global function definition for 'var'
pfa: no visible global function definition for 'cor'
Undefined global functions or variables:
  arrows calibrate circle cor ginv nlminb par plot points rad2degree
  runif textxy var
Consider adding
  importFrom("graphics", "arrows", "par", "plot", "points")
  importFrom("stats", "cor", "nlminb", "runif", "var")
to your NAMESPACE file.
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.
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.
GA_search : subset_score: no visible global function definition for
  'combn'
choose_lambda : subset_score: no visible global function definition for
  'combn'
cond.fyx: no visible global function definition for 'var'
cond.fyx: no visible global function definition for 'cor'
diff_gen_PPI: no visible global function definition for 'cov'
diff_gen_PPI: no visible global function definition for 'sd'
f.test: no visible binding for global variable 'var'
get_quantiles : node_edge: no visible global function definition for
  'combn'
score_scaling: no visible global function definition for 'hist'
score_scaling: no visible global function definition for 'sd'
Undefined global functions or variables:
  combn cor cov hist sd var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "cov", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
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.
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.
CosmoPhotoZestimator: no visible global function definition for
  'predict'
computeCombPCA: no visible global function definition for 'prcomp'
computeDiagPhotoZ: no visible global function definition for 'sd'
computeDiagPhotoZ: no visible global function definition for 'median'
computeDiagPhotoZ: no visible global function definition for 'mad'
glmPredictPhotoZ: no visible global function definition for 'predict'
glmTrainPhotoZ: no visible global function definition for 'glm'
glmTrainPhotoZ: no visible global function definition for 'Gamma'
glmTrainPhotoZ: no visible global function definition for
  'inverse.gaussian'
plotDiagPhotoZ: no visible global function definition for 'median'
plotDiagPhotoZ: no visible global function definition for 'mad'
Undefined global functions or variables:
  Gamma glm inverse.gaussian mad median prcomp predict sd
Consider adding
  importFrom("stats", "Gamma", "glm", "inverse.gaussian", "mad",
             "median", "prcomp", "predict", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Rglpk' 'glmnet' 'parallel' 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
'library' or 'require' calls to packages already attached by Depends:
  'Matrix' 'mlogit' 'poLCA'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Matrix' 'mlogit' 'poLCA'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
covLCA: no visible global function definition for 'model.response'
covLCA: no visible global function definition for 'model.frame'
covLCA: no visible global function definition for 'model.matrix'
covLCA: no visible global function definition for 'rnorm'
covLCA: no visible global function definition for 'flush.console'
covLCA: no visible global function definition for 'ginv'
covLCA.initialAlphaGamma: no visible global function definition for
  'as.formula'
covLCA.initialAlphaGamma: no visible global function definition for
  'mlogit.data'
covLCA.initialAlphaGamma: no visible global function definition for
  'mlogit'
covLCA.initialBeta: no visible global function definition for
  'as.formula'
covLCA.initialBeta: no visible global function definition for 'poLCA'
covLCA.initialBeta: no visible global function definition for
  'mlogit.data'
covLCA.initialBeta: no visible global function definition for 'mlogit'
covLCA.paramVariance: no visible global function definition for 'ginv'
covLCA.varianceFirst: no visible global function definition for 'bdiag'
Undefined global functions or variables:
  as.formula bdiag flush.console ginv mlogit mlogit.data model.frame
  model.matrix model.response poLCA rnorm
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response", "rnorm")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
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.
calcz02: no visible global function definition for 'coxph'
calcz02: no visible global function definition for 'residuals'
covTest: no visible global function definition for 'Surv'
covTest: no visible global function definition for 'predict'
covTest: no visible global function definition for 'update'
covTest: no visible global function definition for 'lsfit'
covTest: no visible global function definition for 'pexp'
covTest: no visible global function definition for 'pf'
lars.en: no visible binding for global variable 'var'
predict.lars.en: no visible global function definition for 'predict'
Undefined global functions or variables:
  Surv coxph lsfit pexp pf predict residuals update var
Consider adding
  importFrom("stats", "lsfit", "pexp", "pf", "predict", "residuals",
             "update", "var")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'parallel' 'snowfall'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Matrix' 'prodlim'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CoxBoost: no visible global function definition for 'Matrix'
CoxBoost: no visible binding for global variable 'sd'
CoxBoost: no visible global function definition for 'predict'
cv.CoxBoost : eval.fold: no visible global function definition for
  'predict'
cv.CoxBoost: no visible global function definition for 'mclapply'
cv.CoxBoost: no visible binding for global variable 'sd'
estimPVal: no visible global function definition for 'mclapply'
iCoxBoost: no visible global function definition for 'terms'
iCoxBoost: no visible global function definition for 'model.response'
iCoxBoost: no visible global function definition for 'model.frame'
iCoxBoost: no visible global function definition for 'model.matrix'
iCoxBoost: no visible global function definition for 'Matrix'
plot.CoxBoost: no visible global function definition for 'plot'
plot.CoxBoost: no visible global function definition for 'lines'
plot.CoxBoost: no visible global function definition for 'text'
predict.iCoxBoost: no visible global function definition for
  'model.response'
predict.iCoxBoost: no visible global function definition for
  'model.frame'
predict.iCoxBoost: no visible global function definition for
  'model.matrix'
Undefined global functions or variables:
  Matrix lines mclapply model.frame model.matrix model.response plot
  predict sd terms text
Consider adding
  importFrom("graphics", "lines", "plot", "text")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "predict", "sd", "terms")
to your NAMESPACE file.
coxaalen: no visible global function definition for 'terms'
coxaalen: no visible global function definition for 'model.matrix'
coxaalen: no visible binding for global variable 'frame'
coxaalen: no visible global function definition for 'update.formula'
coxaalen: no visible global function definition for 'capture.output'
coxdual: no visible global function definition for 'terms'
coxdual: no visible global function definition for 'model.matrix'
coxdual: no visible binding for global variable 'frame'
coxdual: no visible global function definition for 'update.formula'
coxdual: no visible global function definition for 'as.formula'
coxdual: no visible global function definition for 'capture.output'
frame.assign: no visible global function definition for 'model.matrix'
linapprox: no visible global function definition for 'approx'
print.coxinterval: no visible global function definition for 'pchisq'
print.summary.coxinterval : f: no visible global function definition
  for 'printCoefmat'
step2stepfun : f: no visible global function definition for 'stepfun'
summary.coxinterval : f: no visible global function definition for
  'pchisq'
summary.coxinterval : f: no visible global function definition for
  'qnorm'
Undefined global functions or variables:
  approx as.formula capture.output frame model.matrix pchisq
  printCoefmat qnorm stepfun terms update.formula
Consider adding
  importFrom("graphics", "frame")
  importFrom("stats", "approx", "as.formula", "model.matrix", "pchisq",
             "printCoefmat", "qnorm", "stepfun", "terms",
             "update.formula")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
comp.graph: no visible global function definition for 'qnorm'
comp.graph: no visible global function definition for 'plot'
comp.graph: no visible global function definition for 'polygon'
comp.graph: no visible global function definition for 'lines'
cox.ridge: no visible global function definition for 'terms'
cox.ridge: no visible global function definition for 'model.extract'
cox.ridge: no visible global function definition for 'model.matrix'
cox.ridge: no visible binding for global variable 'hat'
Undefined global functions or variables:
  hat lines model.extract model.matrix plot polygon qnorm terms
Consider adding
  importFrom("graphics", "lines", "plot", "polygon")
  importFrom("stats", "hat", "model.extract", "model.matrix", "qnorm",
             "terms")
to your NAMESPACE file.
Package in Depends field not imported from: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
coxr: no visible global function definition for 'model.extract'
coxr: no visible global function definition for 'model.matrix'
coxr.draw: no visible global function definition for 'plot'
coxr.draw: no visible global function definition for 'lines'
coxr.draw: no visible global function definition for 'points'
coxr.fit: no visible global function definition for 'quantile'
gen_data: no visible global function definition for 'rnorm'
gen_data: no visible global function definition for 'rexp'
plot.coxr: no visible global function definition for 'quantile'
plot.coxr: no visible global function definition for 'par'
plot.coxr: no visible global function definition for 'mtext'
plot.coxr: no visible global function definition for 'title'
plot.coxr: no visible global function definition for 'split.screen'
plot.coxr: no visible global function definition for 'screen'
plot.coxr: no visible global function definition for 'close.screen'
print.coxr: no visible global function definition for 'pnorm'
print.coxr: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  close.screen lines model.extract model.matrix mtext par pchisq plot
  pnorm points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par", "plot",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
CumInt : fn: no visible global function definition for 'integrate'
RND0: no visible global function definition for 'runif'
coxseiInt: no visible global function definition for 'approxfun'
coxseiInt : js: no visible global function definition for 'tail'
coxseiest: no visible global function definition for 'approxfun'
coxseiest : loglik : ll: no visible global function definition for
  'tail'
coxseiest: no visible global function definition for 'optim'
coxseiest2: no visible global function definition for 'approxfun'
coxseiest2: no visible global function definition for 'optim'
coxseiest3: no visible global function definition for 'approxfun'
coxseiest3: no visible global function definition for 'optim'
coxseiexp: no visible global function definition for 'approxfun'
coxseiexp: no visible global function definition for 'optim'
coxseiexp : js: no visible global function definition for 'tail'
coxseiexp: no visible global function definition for 'pnorm'
coxseiexp: no visible global function definition for 'stepfun'
coxseifit.ex: no visible global function definition for 'approxfun'
coxseifit.ex: no visible global function definition for 'optim'
coxseifit.ex : js: no visible global function definition for 'tail'
coxseifit.ex: no visible global function definition for 'pnorm'
coxseifit.ex: no visible global function definition for 'stepfun'
coxseisim : int.at.lasttm: no visible global function definition for
  'tail'
plot.coxsei: no visible global function definition for 'plot'
print.summary.coxsei: no visible global function definition for
  'printCoefmat'
summary.coxsei: no visible global function definition for 'coef'
Undefined global functions or variables:
  approxfun coef integrate optim plot pnorm printCoefmat runif stepfun
  tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "approxfun", "coef", "integrate", "optim", "pnorm",
             "printCoefmat", "runif", "stepfun")
  importFrom("utils", "tail")
to your NAMESPACE file.
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 in Depends field not imported from:
  'rms' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
phcpe: no visible global function definition for 'model.matrix'
phcpe: no visible global function definition for 'sd'
phcpe2: no visible global function definition for 'sd'
Undefined global functions or variables:
  model.matrix sd
Consider adding
  importFrom("stats", "model.matrix", "sd")
to your NAMESPACE file.
QR.cd: no visible global function definition for 'quantile'
QR.lasso.cd: no visible global function definition for 'quantile'
cqr.cd: no visible global function definition for 'quantile'
cqr.lasso.cd: no visible global function definition for 'quantile'
cqr.lasso.mm: no visible global function definition for 'quantile'
cqr.mm: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
distance.comoving: no visible global function definition for
  'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
.cramer.kritwertfft: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
crantastic.submitInstalledPackages: no visible global function
  definition for 'installed.packages'
postData: no visible global function definition for 'make.socket'
postData: no visible global function definition for 'write.socket'
postData: no visible global function definition for 'read.socket'
postData: no visible global function definition for 'close.socket'
Undefined global functions or variables:
  close.socket installed.packages make.socket read.socket write.socket
Consider adding
  importFrom("utils", "close.socket", "installed.packages",
             "make.socket", "read.socket", "write.socket")
to your NAMESPACE file.
catrandpvalue: no visible global function definition for 'read.table'
catrandpvalue: no visible global function definition for 'rmultinom'
catrandpvaluepermute: no visible global function definition for
  'read.table'
catrandstat: no visible global function definition for 'stack'
catrandstat: no visible global function definition for 'pchisq'
catrandstat: no visible binding for global variable 'var'
Undefined global functions or variables:
  pchisq read.table rmultinom stack var
Consider adding
  importFrom("stats", "pchisq", "rmultinom", "var")
  importFrom("utils", "read.table", "stack")
to your NAMESPACE file.
cm.CVaR: no visible global function definition for 'quantile'
cm.hist: no visible global function definition for 'hist'
cm.quantile: no visible global function definition for 'qnorm'
cm.rnorm: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  hist qnorm quantile rnorm
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
makeX_eset: no visible global function definition for 'model.matrix'
normFit: no visible binding for global variable 'lm'
normFit: no visible binding for global variable 'sd'
normFit: no visible global function definition for 'lm'
normPred: no visible binding for global variable 'predict'
normPred: no visible global function definition for 'predict'
normPred: no visible binding for global variable 'median'
plot.nFit: no visible global function definition for 'par'
plot.nFit: no visible global function definition for 'barplot'
plot.nFit: no visible global function definition for 'legend'
show_nfit: no visible global function definition for 'anova'
show_nfit: no visible global function definition for 'residuals'
show_nfit: no visible global function definition for 'fitted'
standardsFit: no visible binding for global variable 'lm'
standardsFit: no visible global function definition for 'resid'
standardsFit: no visible global function definition for
  'compareVersion'
standardsPred: no visible global function definition for 'predict'
makeX,ExpressionSet-character: no visible global function definition
  for 'model.matrix'
plot,nFit: no visible global function definition for 'par'
plot,nFit: no visible global function definition for 'barplot'
plot,nFit: no visible global function definition for 'legend'
show,nFit: no visible global function definition for 'anova'
show,nFit: no visible global function definition for 'residuals'
show,nFit: no visible global function definition for 'fitted'
Undefined global functions or variables:
  anova barplot compareVersion fitted legend lm median model.matrix par
  predict resid residuals sd
Consider adding
  importFrom("graphics", "barplot", "legend", "par")
  importFrom("stats", "anova", "fitted", "lm", "median", "model.matrix",
             "predict", "resid", "residuals", "sd")
  importFrom("utils", "compareVersion")
to your NAMESPACE file.
CRMoneIncomplete: no visible global function definition for 'runif'
CRMoneIncomplete: no visible global function definition for 'rexp'
CRMsimOne: no visible global function definition for 'runif'
CRMsimOne: no visible global function definition for 'rexp'
CRMtwoIncomplete: no visible global function definition for 'runif'
CRMtwoIncomplete: no visible global function definition for 'rexp'
Undefined global functions or variables:
  rexp runif
Consider adding
  importFrom("stats", "rexp", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'RCurl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RCurl' 'chron'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
collateDaily: no visible global function definition for 'read.table'
collateDaily: no visible global function definition for 'write.table'
collateHourly: no visible global function definition for 'read.table'
collateHourly: no visible global function definition for 'write.table'
downloadCRN: no visible global function definition for 'download.file'
getUrlsCRN: no visible global function definition for 'getURL'
writeDataset: no visible global function definition for 'read.table'
writeDataset: no visible global function definition for 'write.table'
Undefined global functions or variables:
  download.file getURL read.table write.table
Consider adding
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
get.plan: no visible global function definition for 'menu'
Undefined global functions or variables:
  menu
Consider adding
  importFrom("utils", "menu")
to your NAMESPACE file.
crossmatchtest: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
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.
'::' or ':::' import not declared from: 'magrittr'
Warning: no function found corresponding to methods exports from 'CR' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
curerate : cr: no visible global function definition for 'rbinom'
curerate : cr: no visible global function definition for 'rexp'
curerate : cr: no visible global function definition for 'runif'
curerate: no visible global function definition for 'new'
showcr: no visible global function definition for 'show'
Undefined global functions or variables:
  new rbinom rexp runif show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "rbinom", "rexp", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
crrp: no visible global function definition for 'approx'
gcrrp: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx
Consider adding
  importFrom("stats", "approx")
to your NAMESPACE file.
crrc: no visible binding for global variable 'na.omit'
crrs: no visible binding for global variable 'na.omit'
mycrr: no visible binding for global variable 'na.omit'
mycrr.test: no visible binding for global variable 'na.omit'
print.crrs: no visible global function definition for 'pnorm'
psh.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  na.omit pchisq pnorm
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pnorm")
to your NAMESPACE file.
crrstep : crr.makecov1: no visible global function definition for
  'model.matrix'
crrstep : crr.dropterm: no visible global function definition for
  'terms'
crrstep : crr.dropterm: no visible global function definition for
  'as.formula'
crrstep : crr.addterm: no visible global function definition for
  'terms'
crrstep : crr.addterm: no visible global function definition for
  'as.formula'
crrstep: no visible global function definition for 'as.formula'
crrstep: no visible global function definition for 'terms'
crrstep: no visible global function definition for 'model.frame'
crrstep: no visible binding for global variable 'na.pass'
crrstep: no visible global function definition for 'update'
crrstep: no visible global function definition for 'drop.terms'
Undefined global functions or variables:
  as.formula drop.terms model.frame model.matrix na.pass terms update
Consider adding
  importFrom("stats", "as.formula", "drop.terms", "model.frame",
             "model.matrix", "na.pass", "terms", "update")
to your NAMESPACE file.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
pielou: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: 'compiler'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
csSAM: no visible binding for global variable 'quantile'
csSAM: no visible global function definition for 'median'
csfit: no visible global function definition for 'lsfit'
csfit: no visible global function definition for 'ls.diag'
plotCsSAM: no visible global function definition for 'pdf'
plotCsSAM: no visible global function definition for 'par'
plotCsSAM: no visible global function definition for 'plot'
plotCsSAM: no visible global function definition for 'title'
plotCsSAM: no visible global function definition for 'dev.off'
runSAM: no visible binding for global variable 'median'
runSAM: no visible global function definition for 'quantile'
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf plot quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
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.
map.coltypes: 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.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    doc    4.1Mb
    libs   5.9Mb
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    extdata  31.9Mb
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'lars' which was already attached by Depends.
  Please remove these calls from your code.
jumpoints : seg.lm.fit0: no visible global function definition for
  'lm.fit'
jumpoints : seg.lm.fit0: no visible global function definition for
  'coef'
jumpoints: no visible global function definition for 'quantile'
jumpoints: no visible global function definition for 'coef'
plot.aCGHsegmented: no visible global function definition for 'plot'
plot.aCGHsegmented: no visible global function definition for 'grey'
plot.aCGHsegmented: no visible global function definition for 'abline'
plot.aCGHsegmented: no visible global function definition for 'points'
plot.aCGHsegmented: no visible global function definition for
  'segments'
plot.aCGHsegmented: no visible global function definition for 'par'
Undefined global functions or variables:
  abline coef grey lm.fit par plot points quantile segments
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
  importFrom("stats", "coef", "lm.fit", "quantile")
to your NAMESPACE file.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File 'curl/libs/i386/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
cci.nostrat: no visible global function definition for 'quantile'
cci.nostrat: no visible global function definition for 'plot'
cci.nostrat: no visible global function definition for 'axis'
cci.nostrat: no visible global function definition for 'lines'
cci.nostrat: no visible global function definition for 'legend'
cci.strat: no visible global function definition for 'plot'
cci.strat: no visible global function definition for 'axis'
cci.strat: no visible global function definition for 'lines'
cci.strat: no visible global function definition for 'legend'
clfs.nostrat: no visible global function definition for 'quantile'
clfs.nostrat: no visible global function definition for 'plot'
clfs.nostrat: no visible global function definition for 'axis'
clfs.nostrat: no visible global function definition for 'lines'
clfs.nostrat: no visible global function definition for 'legend'
clfs.strat: no visible global function definition for 'plot'
clfs.strat: no visible global function definition for 'axis'
clfs.strat: no visible global function definition for 'lines'
clfs.strat: no visible global function definition for 'legend'
pvals.2cat: no visible global function definition for 'pchisq'
pvals.cat: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  axis legend lines pchisq plot quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
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.
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.
ci.cvAUC: no visible global function definition for 'qnorm'
ci.pooled.cvAUC: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
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.
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').
cvimpute.by.wavelet: no visible global function definition for 'sd'
cvimpute.by.wavelet: no visible global function definition for 'mad'
cvimpute.image.by.wavelet: no visible global function definition for
  'sd'
cvimpute.image.by.wavelet: no visible global function definition for
  'mad'
cvwavelet.image.after.impute: no visible global function definition for
  'sd'
cvwavelet.image.after.impute: no visible global function definition for
  'mad'
Undefined global functions or variables:
  mad sd
Consider adding
  importFrom("stats", "mad", "sd")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'robustbase'
A package should be listed in only one of these fields.
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.
create_clustering_problem: no visible global function definition for
  'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   1.9Mb
.mixgauss_init: no visible global function definition for 'cov'
.mixgauss_init: no visible global function definition for 'var'
Undefined global functions or variables:
  cov var
Consider adding
  importFrom("stats", "cov", "var")
to your NAMESPACE file.
cxxfun.from.dll: no visible global function definition for 'new'
cxxfun.from.dso.bin: no visible global function definition for 'new'
cxxfunctionplus: no visible global function definition for 'getPlugin'
cxxfunctionplus: no visible global function definition for
  'cxxfunction'
cxxfunctionplus: no visible global function definition for 'new'
show,cxxdso: no visible global function definition for 'object.size'
Undefined global functions or variables:
  cxxfunction getPlugin new object.size
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package in Depends field not imported from: 'fda'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.for.sequence.endpoint.breaks: no visible global function
  definition for 'na.omit'
get.breaks.vector: no visible global function definition for 'na.omit'
get.cycle.breaks: no visible global function definition for 'na.omit'
get.cycle.counts: no visible global function definition for 'na.omit'
get.cycle.matrix: no visible global function definition for 'na.omit'
get.cycle.minimums: no visible global function definition for 'na.omit'
get.peaks: no visible global function definition for 'embed'
get.trans: no visible global function definition for
  'create.bspline.basis'
get.trans: no visible global function definition for 'smooth.basis'
get.trans: no visible global function definition for 'deriv.fd'
get.trans: no visible global function definition for 'eval.fd'
get.transition.locations: no visible global function definition for
  'na.omit'
get.transition.locations.FDiff: no visible global function definition
  for 'na.omit'
get.window: no visible global function definition for 'sd'
Undefined global functions or variables:
  create.bspline.basis deriv.fd embed eval.fd na.omit sd smooth.basis
Consider adding
  importFrom("stats", "embed", "na.omit", "sd")
to your NAMESPACE file.
cytoDiv: no visible global function definition for 'colorRampPalette'
cytoDiv: no visible global function definition for 'persp'
Undefined global functions or variables:
  colorRampPalette persp
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "persp")
to your NAMESPACE file.
'::' or ':::' import not declared from: 'httr'
compareModels: no visible binding for global variable 'fgl'
compareModels: no visible global function definition for 'rlm'
compareModels: no visible global function definition for 'lm'
compareModels: no visible global function definition for 'predict'
compareModels: no visible global function definition for 'resid'
plotSampDist: no visible global function definition for 'par'
plotSampDist: no visible global function definition for 'density'
plotSampDist: no visible global function definition for 'plot'
plotSampDist: no visible global function definition for 'lines'
plotSampDist: no visible global function definition for 'legend'
plotSampDist: no visible global function definition for 'qqnorm'
plotSampDist: no visible global function definition for 'points'
plotSampDist: no visible global function definition for 'mtext'
simulateSampDist: no visible binding for global variable 'rnorm'
Undefined global functions or variables:
  density fgl legend lines lm mtext par plot points predict qqnorm
  resid rlm rnorm
Consider adding
  importFrom("graphics", "legend", "lines", "mtext", "par", "plot",
             "points")
  importFrom("stats", "density", "lm", "predict", "qqnorm", "resid",
             "rnorm")
to your NAMESPACE file.
Package in Depends field not imported from: 's20x'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
allCombs: no visible global function definition for 'combn'
brute.search: no visible global function definition for 'na.omit'
dag.draw: no visible global function definition for 'plot'
dag.draw: no visible global function definition for 'text'
dag.init: no visible global function definition for
  'installed.packages'
dag.legend: no visible global function definition for 'text'
dag.letter: no visible global function definition for 'text'
dag.move: no visible global function definition for 'identify'
dag.move: no visible global function definition for 'locator'
dag.sim: no visible global function definition for 'rnorm'
dag.sim: no visible global function definition for 'rbinom'
dag.sim : <anonymous>: no visible global function definition for
  'rbinom'
garrows: no visible global function definition for 'arrows'
smoothArc: no visible global function definition for 'points'
summary_dagRdag: no visible global function definition for 'na.omit'
viv: no visible global function definition for 'na.omit'
write.paths: no visible global function definition for 'text'
Undefined global functions or variables:
  arrows combn identify installed.packages locator na.omit plot points
  rbinom rnorm text
Consider adding
  importFrom("graphics", "arrows", "identify", "locator", "plot",
             "points", "text")
  importFrom("stats", "na.omit", "rbinom", "rnorm")
  importFrom("utils", "combn", "installed.packages")
to your NAMESPACE file.
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.
DAMOCLES_ML: no visible global function definition for 'flush.console'
DAMOCLES_bootstrap: no visible global function definition for
  'cophenetic'
DAMOCLES_bootstrap: no visible global function definition for 'sd'
DAMOCLES_bootstrap: no visible global function definition for
  'quantile'
DAMOCLES_sim: no visible global function definition for 'na.omit'
DAMOCLES_sim: no visible global function definition for 'runif'
DAMOCLES_sim: no visible global function definition for 'lines'
DAMOCLES_sim: no visible global function definition for 'rnorm'
DAMOCLES_sim: no visible global function definition for 'dexp'
DAMOCLES_sim: no visible global function definition for 'dist'
DAMOCLES_simplex: no visible global function definition for
  'flush.console'
Undefined global functions or variables:
  cophenetic dexp dist flush.console lines na.omit quantile rnorm runif
  sd
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "cophenetic", "dexp", "dist", "na.omit",
             "quantile", "rnorm", "runif", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
drawAimSpot: no visible global function definition for 'points'
drawBoard: no visible global function definition for 'par'
drawBoard: no visible global function definition for 'plot'
drawBoard: no visible global function definition for 'points'
drawBoard: no visible global function definition for 'text'
drawHeatmap: no visible global function definition for 'heat.colors'
drawHeatmap: no visible global function definition for 'par'
drawHeatmap: no visible global function definition for 'image'
drawHeatmap: no visible global function definition for 'rect'
generalExpScores: no visible global function definition for 'fft'
simpleExpScores: no visible global function definition for 'mvfft'
simpleExpScores: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft heat.colors image mvfft par plot points rect text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "points", "rect",
             "text")
  importFrom("stats", "fft", "mvfft")
to your NAMESPACE file.
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.
datadict.profile: no visible global function definition for
  'txtProgressBar'
datadict.profile: no visible global function definition for
  'setTxtProgressBar'
datadict_profile: no visible global function definition for
  'txtProgressBar'
datadict_profile: no visible global function definition for
  'setTxtProgressBar'
heatmap.quality: no visible global function definition for
  'colorRampPalette'
heatmap.quality: no visible global function definition for 'heatmap'
heatmap_quality: no visible global function definition for
  'colorRampPalette'
heatmap_quality: no visible global function definition for 'heatmap'
is.oneOf: no visible global function definition for 'read.csv'
is_one_of: no visible global function definition for 'read.csv'
pkg.version: no visible global function definition for 'citation'
pkg_version: no visible global function definition for 'citation'
ruleCoverage: no visible global function definition for 'dotchart'
ruleCoverage: no visible global function definition for 'abline'
rule_coverage: no visible global function definition for 'dotchart'
rule_coverage: no visible global function definition for 'abline'
scoreSum: no visible global function definition for 'plot'
score_sum: no visible global function definition for 'plot'
shortSummary: no visible global function definition for 'sd'
short_summary: no visible global function definition for 'sd'
Undefined global functions or variables:
  abline citation colorRampPalette dotchart heatmap plot read.csv sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "dotchart", "plot")
  importFrom("stats", "heatmap", "sd")
  importFrom("utils", "citation", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Package suggested but not available for checking: 'Rhipe'
'library' or 'require' call not declared from: 'lattice'
Package in Depends field not imported from: 'DBI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onLoad : <anonymous>: no visible global function definition for
  'read.table'
.onLoad : <anonymous>: no visible global function definition for
  'dbConnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbListTables'
.onLoad : <anonymous>: no visible global function definition for
  'dbExistsTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbReadTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbWriteTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbDisconnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbRemoveTable'
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in 'dataone-Ex.R' failed
The error most likely occurred in:

> ### Name: listObjects
> ### Title: Retrieve the list of objects that match the search parameters
> ### Aliases: listObjects listObjects,D1Node-method
> 
> ### ** Examples
> 
> library(dataone)
> cn <- CNode("STAGING")
> fromDate <- "2013-01-01T01:01:01.000+00:00"
> toDate <- "2015-12-31T01:01:01.000+00:00"
> formatId <- "eml://ecoinformatics.org/eml-2.1.0"
> start <- 0
> count <- 5
> objects <- listObjects(cn, fromDate=fromDate, toDate=toDate, 
+     formatId=formatId, start=start, count=count)
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 14 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 14 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2
Execution halted
'library' or 'require' call not declared from: 'xml2'
checkDataQuality: no visible binding for global variable 'quantile'
checkDataQuality: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  quantile write.csv
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.6Mb
browse: no visible global function definition for 'slot'
browse: no visible global function definition for 'page'
default.options: no visible binding for global variable 'object.size'
heat.view: no visible global function definition for 'head'
heat.view: no visible global function definition for 'tail'
whos: no visible global function definition for 'slotNames'
whos : <anonymous> : <anonymous>: no visible global function definition
  for 'slot'
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Depends: includes the non-default packages:
  'xtable' 'akima' 'R.oo' 'R.methodsS3' 'matlab' 'lattice' 'locfit'
  'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'R.methodsS3' 'R.oo' 'akima' 'graphics' 'grid' 'lattice' 'locfit'
  'matlab' 'xtable'
  Please remove these calls from your code.
'library' or 'require' call to 'R.matlab' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'R.methodsS3' 'R.oo' 'akima' 'grid' 'lattice' 'locfit' 'matlab'
  'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DAT : DATrun : calch: no visible global function definition for
  'preplot'
DAT : DATrun: no visible global function definition for 'rot90'
DAT : DATrun: no visible global function definition for 'median'
DAT : DATrun: no visible global function definition for 'locfit.robust'
DAT : DATrun: no visible global function definition for 'preplot'
DAT : DATrun: no visible global function definition for 'dev.new'
DAT : DATrun: no visible global function definition for 'image'
DAT : DATrun: no visible global function definition for 'palette'
DAT : DATrun: no visible global function definition for
  'colorRampPalette'
DAT : DATrun: no visible global function definition for 'text'
DAT : DATrun: no visible global function definition for 'dev.set'
DAT : DATrun: no visible global function definition for 'locator'
DAT : DATrun: no visible global function definition for 'graphics.off'
DAT : DATrun: no visible global function definition for 'pdf'
DAT : DATrun: no visible global function definition for 'layout'
DAT : DATrun: no visible global function definition for 'par'
DAT : DATrun: no visible global function definition for 'plot'
DAT : DATrun: no visible global function definition for 'frame'
DAT : DATrun: no visible global function definition for 'lines'
DAT : DATrun: no visible global function definition for 'dev.off'
DAT : DATrun: no visible global function definition for 'writeMat'
DAT: no visible binding for global variable 'DAT.simData'
Undefined global functions or variables:
  DAT.simData colorRampPalette dev.new dev.off dev.set frame
  graphics.off image layout lines locator locfit.robust median palette
  par pdf plot preplot rot90 text writeMat
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "dev.set", "graphics.off", "palette", "pdf")
  importFrom("graphics", "frame", "image", "layout", "lines", "locator",
             "par", "plot", "text")
  importFrom("stats", "median", "preplot")
to your NAMESPACE file.
'::' or ':::' import not declared from: 'lme4'
'library' or 'require' calls to packages already attached by Depends:
  'RMySQL' 'gWidgets'
  Please remove these calls from your code.
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.
computePval: no visible global function definition for 'lm'
computeQhat: no visible global function definition for 'pnorm'
dbELnorm: no visible global function definition for 'rnorm'
getCutoffTableThree: no visible global function definition for 'lm'
getCutoffTableTwo: no visible global function definition for 'lm'
getCutoffValue: no visible global function definition for 'lm'
helperGetTstat: no visible global function definition for 'rnorm'
returnCutoffValue: no visible global function definition for 'rnorm'
returnCutoffValue: no visible global function definition for 'quantile'
varianceEstimator: no visible global function definition for 'density'
varianceEstimator: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  density ecdf lm pnorm quantile rnorm
Consider adding
  importFrom("stats", "density", "ecdf", "lm", "pnorm", "quantile",
             "rnorm")
to your NAMESPACE file.
'library' or 'require' call to 'fdrtool' which was already attached by Depends.
  Please remove these calls from your code.
avelinkdis: no visible global function definition for 'sd'
avelinkdis: no visible global function definition for 'dist'
centdis: no visible global function definition for 'sd'
centdis: no visible global function definition for 'dist'
distable: no visible global function definition for 'write.table'
functionall: no visible global function definition for 'read.table'
randdis: no visible global function definition for 'write.table'
valuep: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  dist read.table sd write.csv write.table
Consider adding
  importFrom("stats", "dist", "sd")
  importFrom("utils", "read.table", "write.csv", "write.table")
to your NAMESPACE file.
'::' or ':::' import not declared from: 'withr'
.CA.fast2: no visible global function definition for 'lsfit'
.T2.fast: no visible global function definition for 'txtProgressBar'
.T2.fast: no visible global function definition for 'setTxtProgressBar'
.dcemri.bayes: no visible global function definition for 'median'
.dcemri.bayes: no visible global function definition for 'sd'
.dcemri.map : posterior: no visible global function definition for
  'dnorm'
.dcemri.map : posterior: no visible global function definition for
  'dgamma'
.dcemri.map : posterior: no visible global function definition for
  'dbeta'
.dcemri.map.single: no visible global function definition for 'optim'
.dcemri.spline: no visible binding for global variable 'median'
.dcemri.spline: no visible global function definition for 'median'
.dcemri.spline.single: no visible binding for global variable
  'quantile'
.dcemri.spline.single: no visible binding for global variable 'median'
.dcemri.spline.single: no visible global function definition for
  'median'
.ftm: no visible global function definition for 'fft'
.ftm: no visible global function definition for 'matplot'
.ftm: no visible global function definition for 'legend'
compartmentalModel : <anonymous>: no visible global function definition
  for 'approx'
convFFT: no visible global function definition for 'fft'
extractAIF : c.start: no visible global function definition for 'sd'
extractAIF : c.start: no visible global function definition for 'cor'
Undefined global functions or variables:
  approx cor dbeta dgamma dnorm fft legend lsfit matplot median optim
  quantile sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cor", "dbeta", "dgamma", "dnorm", "fft",
             "lsfit", "median", "optim", "quantile", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Packages in Depends field not imported from:
  'lattice' 'latticeExtra'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DrawAlphas: no visible global function definition for 'rmultinom'
DrawClasses: no visible global function definition for 'runif'
GetGammaNames: no visible global function definition for 'combn'
GetLambdaNamesForItem: no visible global function definition for
  'combn'
SampleParameterEstimates: no visible global function definition for
  'rnorm'
plot,attribute.class-missing: no visible binding for global variable
  'attr.number'
plot,attribute.class-missing: no visible binding for global variable
  'mean.attr'
plot,attribute.profile.class-missing: no visible binding for global
  variable 'attr.profile.number'
plot,attribute.profile.class-missing: no visible binding for global
  variable 'mean.attr.profile'
summary,attribute.class: no visible binding for global variable 'value'
summary,attribute.profile.class: no visible binding for global variable
  'max.class'
Undefined global functions or variables:
  attr.number attr.profile.number combn max.class mean.attr
  mean.attr.profile rmultinom rnorm runif value
Consider adding
  importFrom("stats", "rmultinom", "rnorm", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
test.LM: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
getDelimiter: no visible global function definition for 'read.csv'
setupfile: no visible global function definition for 'read.csv'
treatPath: no visible global function definition for 'file_test'
Undefined global functions or variables:
  file_test read.csv
Consider adding
  importFrom("utils", "file_test", "read.csv")
to your NAMESPACE file.
ifft: no visible global function definition for 'fft'
lines.deamer: no visible global function definition for 'lines'
plot.deamer: no visible global function definition for 'plot'
rlaplace: no visible global function definition for 'runif'
Undefined global functions or variables:
  fft lines plot runif
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
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 'plot'
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 plot pnorm qchisq sd
  vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
DeconCPdf: no visible global function definition for 'bw.nrd0'
DeconCPdf: no visible global function definition for 'bw.nrd'
DeconCPdf: no visible global function definition for 'bw.ucv'
DeconCPdf: no visible global function definition for 'bw.bcv'
DeconCPdf: no visible global function definition for 'bw.SJ'
DeconCPdf: no visible global function definition for 'density'
DeconCPdf: no visible global function definition for 'dnorm'
bw.dboot2 : suppL2: no visible global function definition for 'density'
bw.dboot2 : suppL2: no visible global function definition for 'rnorm'
bw.dboot2 : gaussL2: no visible global function definition for
  'density'
bw.dboot2 : gaussL2: no visible global function definition for 'rnorm'
bw.dmise: no visible global function definition for 'var'
plot.Decon: no visible global function definition for 'plot.default'
plot.Decon: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm plot.default
  rnorm var
Consider adding
  importFrom("graphics", "abline", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "rnorm", "var")
to your NAMESPACE file.
'library' or 'require' call to 'irr' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.make3dScatterPlotDialog: no visible global function definition for
  'install.packages'
.makePackageDataDialog: no visible global function definition for
  'data'
.makeVignetteDialog: no visible global function definition for
  'vignette'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible binding for global variable 'winMenuAddItem'
.onLoad: no visible binding for global variable 'jgr.addMenuItem'
.onLoad : gui.addSeperator: no visible global function definition for
  'jgr.addMenuSeparator'
applyModel: no visible global function definition for 'predict'
predict.kmeans : <anonymous>: no visible global function definition for
  'dist'
Undefined global functions or variables:
  data dist install.packages jgr.addMenuItem jgr.addMenuSeparator
  predict vignette winMenuAdd winMenuAddItem
Consider adding
  importFrom("stats", "dist", "predict")
  importFrom("utils", "data", "install.packages", "vignette",
             "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file.
Package in Depends field not imported from: 'Deducer'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
'library' or 'require' call to 'klaR' which was already attached by Depends.
  Please remove these calls from your code.
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'new'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'new'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'new'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'new'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'new'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava winMenuAdd winMenuAddItem
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Depends: includes the non-default packages:
  'JavaGD' 'Deducer' 'sp' 'maptools' 'OpenStreetMap' 'scales' 'rgdal'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'UScensus2010'
A package should be listed in only one of these fields.
'library' or 'require' call to 'UScensus2010' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'JavaGD' 'OpenStreetMap' 'maptools' 'rgdal' 'scales' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.makeQuickWordcloud: no visible global function definition for 'J'
.makeQuickWordcloud: no visible global function definition for 'new'
.makeQuickWordcloud: no visible global function definition for '.jnull'
.makeTextPlot: no visible global function definition for 'J'
.makeTextPlot: no visible global function definition for 'new'
.makeTextPlot: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.jnew'
.onLoad: no visible global function definition for 'J'
make.color.scale: no visible global function definition for 'rgb'
Undefined global functions or variables:
  .jnew .jnull .jpackage J new rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
DEEPR : perm_function: no visible global function definition for 'head'
DEEPR : perm_function: no visible global function definition for 'tail'
simCophy: no visible global function definition for 'rpois'
simCophy: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  head rmultinom rpois tail
Consider adding
  importFrom("stats", "rmultinom", "rpois")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
kern: no visible global function definition for 'var'
kern: no visible global function definition for 'dnorm'
pdeg: no visible global function definition for 'var'
pdeg: no visible global function definition for 'dnorm'
z.b: no visible binding for global variable 'var'
z.s: no visible binding for global variable 'var'
Undefined global functions or variables:
  dnorm var
Consider adding
  importFrom("stats", "dnorm", "var")
to your NAMESPACE file.
bootbagg: no visible global function definition for 'runif'
bootworpl: no visible global function definition for 'runif'
des12: no visible global function definition for 'rnorm'
des12: no visible global function definition for 'runif'
eval.stage.gauss: no visible global function definition for 'var'
plotparti: no visible global function definition for 'plot'
plotparti: no visible global function definition for 'lines'
plotpartilev: no visible global function definition for 'plot'
plotpartilev: no visible global function definition for 'polygon'
plotpartilev: no visible global function definition for 'points'
simesi: no visible global function definition for 'runif'
simesi3d: no visible global function definition for 'runif'
simfssk: no visible global function definition for 'rnorm'
simfssk: no visible global function definition for 'runif'
simmix.delt: no visible global function definition for 'rnorm'
simmix.delt: no visible global function definition for 'runif'
simpp: no visible global function definition for 'rnorm'
simpp: no visible global function definition for 'runif'
simutree: no visible global function definition for 'runif'
stage.gaussR: no visible global function definition for 'var'
unidis: no visible global function definition for 'runif'
Undefined global functions or variables:
  lines plot points polygon rnorm runif var
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Bootstrapping.CI: no visible global function definition for 'quantile'
D.Jost: no visible global function definition for 'read.table'
D.Jost: no visible global function definition for 'write.table'
Dv.locis.corrected.calc: no visible global function definition for
  'p.adjust'
Gst.Nei: no visible global function definition for 'read.table'
Gst.Nei: no visible global function definition for 'write.table'
H.out: no visible global function definition for 'write.table'
Hardy.calc: no visible global function definition for 'chisq.test'
critical.ci.values: no visible global function definition for
  'quantile'
inputformat: no visible global function definition for 'read.table'
inputformat: no visible global function definition for 'write.table'
over.all.pops: no visible global function definition for 'write.table'
p.value.correcture: no visible global function definition for
  'p.adjust'
pair.pops: no visible global function definition for 'write.table'
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
DEMIPathway: no visible global function definition for 'dhyper'
DEMIPathway: no visible global function definition for 'p.adjust'
calcHypergeoExon: no visible global function definition for 'dhyper'
calcHypergeoProb: no visible global function definition for 'dhyper'
demi: no visible global function definition for 'write.table'
demi.t.test: no visible global function definition for 't.test'
demi.wilcox.test: no visible global function definition for
  'wilcox.test'
demi.wilcox.test.fast: no visible global function definition for
  'wilcox.test'
demiequal: no visible global function definition for 'wilcox.test'
wprob: no visible global function definition for 'combn'
diffexp,DEMIDiff: no visible global function definition for 'median'
diffexp,DEMIDiff: no visible global function definition for 'p.adjust'
loadAnnotation,DEMIExperiment-environment: no visible global function
  definition for 'data'
loadBlat,DEMIExperiment-environment: no visible global function
  definition for 'data'
loadCytoband,DEMIExperiment-environment: no visible global function
  definition for 'data'
loadPathway,DEMIExperiment-environment: no visible global function
  definition for 'data'
Undefined global functions or variables:
  combn data dhyper median p.adjust t.test wilcox.test write.table
Consider adding
  importFrom("stats", "dhyper", "median", "p.adjust", "t.test",
             "wilcox.test")
  importFrom("utils", "combn", "data", "write.table")
to your NAMESPACE file.
DendSer: no visible global function definition for 'getFromNamespace'
crit2cost : <anonymous>: no visible global function definition for
  'as.dist'
dser.dist: no visible global function definition for 'hclust'
dser.matrix: no visible global function definition for 'dist'
plotAsColor: no visible global function definition for 'image'
plotAsColor: no visible global function definition for 'box'
plotAsColor: no visible global function definition for 'axis'
seriation_method_dist_dser: no visible global function definition for
  'hclust'
seriation_method_dist_dser: no visible global function definition for
  'modifyList'
seriation_method_leafsort: no visible global function definition for
  'modifyList'
Undefined global functions or variables:
  as.dist axis box dist getFromNamespace hclust image modifyList
Consider adding
  importFrom("graphics", "axis", "box", "image")
  importFrom("stats", "as.dist", "dist", "hclust")
  importFrom("utils", "getFromNamespace", "modifyList")
to your NAMESPACE file.
Package suggested but not available for checking: 'Rdonlp2'
MBD: no visible global function definition for 'par'
MBD: no visible global function definition for 'gray'
MBD: no visible global function definition for 'matplot'
MBD: no visible global function definition for 'polygon'
MBD: no visible global function definition for 'lines'
MBD: no visible global function definition for 'legend'
MBD: no visible global function definition for 'matlines'
R.test: no visible global function definition for 'runif'
R.test: no visible global function definition for 'wilcox.test'
centralPlot: no visible global function definition for 'par'
centralPlot: no visible global function definition for
  'colorRampPalette'
centralPlot: no visible global function definition for 'matplot'
centralPlot: no visible global function definition for 'matlines'
centralPlot: no visible global function definition for 'legend'
scalecurve: no visible global function definition for 'plot'
scalecurve: no visible global function definition for 'lines'
scalecurve: no visible global function definition for 'legend'
tmean: no visible global function definition for 'matplot'
tmean: no visible global function definition for 'matlines'
tmean: no visible global function definition for 'lines'
tmean: no visible global function definition for 'legend'
tmean: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette gray legend lines matlines matplot par plot polygon
  runif wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "legend", "lines", "matlines", "matplot", "par",
             "plot", "polygon")
  importFrom("stats", "runif", "wilcox.test")
to your NAMESPACE file.
'::' or ':::' import not declared from: 'lintr'
'library' or 'require' call not declared from: 'lintr'
Package suggested but not available for checking: 'RDCOMClient'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.4Mb
    libs   2.0Mb
ds: no visible global function definition for 'is.ts'
ds: no visible global function definition for 'frequency'
getds: no visible global function definition for 'resid'
getds: no visible global function definition for 'lm.fit'
getds: no visible global function definition for 'sd'
getds: no visible global function definition for 'var'
getds: no visible global function definition for 'fitted'
Undefined global functions or variables:
  fitted frequency is.ts lm.fit resid sd var
Consider adding
  importFrom("stats", "fitted", "frequency", "is.ts", "lm.fit", "resid",
             "sd", "var")
to your NAMESPACE file.
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 'plot'
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 plot png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  'gurobi' 'Rcplex' 'Rmosek'
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 'plot'
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 'plot'
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 plot points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "plot", "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 in Depends field not imported from: 'dplR'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.get' 'InteractiveDetrending' 'RemoveTrend'
Package in Depends field not imported from: 'ash'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running 'has-devel.R' [2s]
  Running 'test-that.R' [73s]
Running the tests in 'tests/test-that.R' failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  
  Attaching package: 'devtools'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  -- 1. Failure: remote_sha.github_remote returns expected value if remote does ex
  remote_sha(github_remote("hadley/devtools@v1.8.0")) not equal to "ad9aac7b9a522354e1ff363a86f389e32cec181b".
  1/1 mismatches
  x[1]: NA
  y[1]: "ad9aac7b9a522354e1ff363a86f389e32cec181b"
  
  
  == testthat results  ===========================================================
  OK: 400 SKIPPED: 10 FAILED: 1
  1. Failure: remote_sha.github_remote returns expected value if remote does exist (@test-remotes.r#75) 
  
  Error: testthat unit tests failed
  Execution halted
Unexported objects imported by ':::' calls:
  'dexter:::get_resp_data' 'dexter:::qcolors'
  See the note in ?`:::` about the use of this operator.
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for 'rbinom'
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for 'rnorm'
simulate_dataframe : generate_initial: no visible global function
  definition for 'rbinom'
simulate_dataframe: no visible binding for global variable 'randu'
simulate_dataframe: no visible global function definition for 'rbinom'
simulate_dataframe: no visible global function definition for 'rnorm'
simulate_dataframe: no visible global function definition for 'rpois'
simulate_dataframe : add_NAs: no visible global function definition for
  'rbinom'
Undefined global functions or variables:
  randu rbinom rnorm rpois
Consider adding
  importFrom("datasets", "randu")
  importFrom("stats", "rbinom", "rnorm", "rpois")
to your NAMESPACE file.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
makeAdjMatrix: no visible global function definition for 'combn'
plotPosteriorN: no visible global function definition for 'plot'
plotPosteriorN: no visible global function definition for 'title'
plotPosteriorN: no visible global function definition for 'lines'
plotPosteriorN: no visible global function definition for 'legend'
venn3: no visible global function definition for 'plot'
venn3: no visible global function definition for 'runif'
venn3: no visible global function definition for 'points'
venn3: no visible global function definition for 'lines'
venn3: no visible global function definition for 'text'
venn4: no visible global function definition for 'plot'
venn4: no visible global function definition for 'lines'
venn4: no visible global function definition for 'runif'
venn4: no visible global function definition for 'points'
Undefined global functions or variables:
  combn legend lines plot points runif text title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text",
             "title")
  importFrom("stats", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
Running examples in 'dgmb-Ex.R' failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("Tktable") : Tcl package 'Tktable' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "table".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
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.
'::' or ':::' import not declared from: 'reshape2'
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.
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').
Packages in Depends field not imported from:
  'PropCIs' 'gee' 'rootSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
diffpci: no visible global function definition for 'diffpropci.Wald.mp'
diffpci: no visible global function definition for 'diffpropci.mp'
diffpci: no visible global function definition for 'scoreci.mp'
exact.cond : exactci: no visible global function definition for 'qf'
exact.midp : binom.midp : f.low: no visible global function definition
  for 'dbinom'
exact.midp : binom.midp : f.low: no visible global function definition
  for 'pbinom'
exact.midp : binom.midp : f.up: no visible global function definition
  for 'dbinom'
exact.midp : binom.midp : f.up: no visible global function definition
  for 'pbinom'
exact.midp : binom.midp : one.ci: no visible global function definition
  for 'uniroot'
np.nv: no visible global function definition for 'qnorm'
np.t: no visible global function definition for 'qt'
uncond: no visible global function definition for 'qnorm'
wald.cc: no visible global function definition for 'qnorm'
wilson: no visible global function definition for 'qnorm'
wilson: no visible global function definition for 'uniroot.all'
wilson.cc: no visible global function definition for 'qnorm'
wilson.cc: no visible global function definition for 'uniroot.all'
wilson.phi: no visible global function definition for 'qnorm'
wilson.phi: no visible global function definition for 'uniroot.all'
Undefined global functions or variables:
  dbinom diffpropci.Wald.mp diffpropci.mp pbinom qf qnorm qt scoreci.mp
  uniroot uniroot.all
Consider adding
  importFrom("stats", "dbinom", "pbinom", "qf", "qnorm", "qt", "uniroot")
to your NAMESPACE file.
'::' or ':::' imports not declared from:
  'devtools' 'stringr'
rkMethodPlot: no visible global function definition for 'par'
rkMethodPlot: no visible global function definition for 'axis'
rkMethodPlot: no visible global function definition for 'points'
rkMethodPlot: no visible global function definition for 'text'
rkMethodPlot: no visible global function definition for 'segments'
rkimp: no visible global function definition for 'runif'
stability.bruteforce: no visible global function definition for 'plot'
stability.bruteforce: no visible global function definition for
  'points'
stability.bruteforce: no visible global function definition for
  'abline'
stability.multistep: no visible global function definition for 'plot'
stability.multistep: no visible global function definition for 'lines'
stability.multistep: no visible global function definition for
  'polygon'
stability.multistep: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis lines par plot points polygon runif segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "polygon", "segments", "text")
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.6/diffusionMap.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
adapreg: no visible global function definition for 'optimize'
adapreg: no visible global function definition for 'runif'
adapreg.m: no visible global function definition for 'lm'
epsilonCompute: no visible global function definition for 'median'
plot.dmap: no visible global function definition for 'plot'
plot.dmap: no visible global function definition for 'stripchart'
Undefined global functions or variables:
  lm median optimize plot runif stripchart
Consider adding
  importFrom("graphics", "plot", "stripchart")
  importFrom("stats", "lm", "median", "optimize", "runif")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
'library' or 'require' calls to packages already attached by Depends:
  'maptools' 'spatstat' 'spdep'
  Please remove these calls from your code.
fAssocmatrix : fAssocmatrix1: no visible global function definition for
  'coordinates<-'
fAssocplot: no visible global function definition for 'plot'
fAssocplot: no visible global function definition for 'coordinates'
fAssocplot: no visible global function definition for 'text'
fAssocplot: no visible global function definition for 'box'
fDrawfigure: no visible global function definition for 'slot'
fDrawfigure : <anonymous>: no visible global function definition for
  'slot'
fDrawfigure: no visible global function definition for
  'SpatialPolygons'
fDrawfigure: no visible global function definition for 'spsample'
fDrawfigure: no visible global function definition for 'plot'
fDrawfigure: no visible global function definition for 'image'
fDrawfigure: no visible global function definition for
  'colorRampPalette'
fDrawfigure: no visible global function definition for 'points'
fRanXY : <anonymous>: no visible global function definition for 'slot'
fRanXY : <anonymous>: no visible global function definition for
  'spsample'
Undefined global functions or variables:
  SpatialPolygons box colorRampPalette coordinates coordinates<- image
  plot points slot spsample text
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "box", "image", "plot", "points", "text")
  importFrom("methods", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  'Rcpp' 'igraph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aLine: no visible global function definition for 'lines'
aLine: no visible global function definition for 'ecdf'
dip.test: no visible global function definition for 'complete.cases'
dip.test: no visible global function definition for 'runif'
dip.test: no visible global function definition for 'approx'
plot.dip: no visible global function definition for 'par'
plot.dip: no visible global function definition for 'ecdf'
plot.dip: no visible global function definition for 'plot'
plot.dip: no visible global function definition for 'title'
plot.dip: no visible global function definition for 'abline'
plot.dip: no visible global function definition for 'axis'
plot.dip: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline approx axis complete.cases ecdf legend lines par plot runif
  title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "approx", "complete.cases", "ecdf", "runif")
to your NAMESPACE file.
nullTest: no visible global function definition for 'rmultinom'
rdirichlet: no visible global function definition for 'rgamma'
simPop: no visible global function definition for 'rnorm'
simPop: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  rgamma rmultinom rnorm
Consider adding
  importFrom("stats", "rgamma", "rmultinom", "rnorm")
to your NAMESPACE file.
rdisclap: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
value: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RUnit' 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mix.distlist.facing.gamma : <anonymous>: no visible global function
  definition for 'dgamma'
mix.distlist.norm: no visible binding for global variable 'dnorm'
mix.mle: no visible global function definition for 'sd'
mix.mle: no visible global function definition for 'quantile'
mix.mle: no visible global function definition for 'median'
mix.mle: no visible global function definition for 'optim'
mix.synthetic.facing.gamma: no visible global function definition for
  'runif'
mix.synthetic.facing.gamma: no visible global function definition for
  'rgamma'
mix.synthetic.normal: no visible global function definition for 'runif'
mix.synthetic.normal: no visible global function definition for 'rnorm'
plot.discrimARTs: no visible global function definition for 'hist'
plot.discrimARTs: no visible global function definition for 'points'
plot.discrimARTs: no visible global function definition for 'lines'
plot.discrimARTs: no visible global function definition for 'grid.text'
plot.discrimARTs: no visible global function definition for 'gpar'
Undefined global functions or variables:
  dgamma dnorm gpar grid.text hist lines median optim points quantile
  rgamma rnorm runif sd
Consider adding
  importFrom("graphics", "hist", "lines", "points")
  importFrom("stats", "dgamma", "dnorm", "median", "optim", "quantile",
             "rgamma", "rnorm", "runif", "sd")
to your NAMESPACE file.
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 in Depends field not imported from:
  'car' 'prettyGraphs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Chi2DistanceFromSort: no visible global function definition for
  'model.matrix'
GraphDistatisAll: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisBoot: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisBoot: no visible global function definition for
  'dataEllipse'
GraphDistatisBoot: no visible global function definition for
  'peeledHull'
GraphDistatisCompromise: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisCompromise: no visible global function definition for
  'prettyPlot'
GraphDistatisPartial: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisPartial: no visible global function definition for
  'points'
GraphDistatisPartial: no visible global function definition for
  'prettyPlot'
GraphDistatisRv: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisRv: no visible global function definition for 'prettyPlot'
Undefined global functions or variables:
  createColorVectorsByDesign dataEllipse model.matrix peeledHull points
  prettyPlot
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "model.matrix")
to your NAMESPACE file.
dist.multiPhylo: no visible global function definition for 'as.dist'
gromov.hyperbolicity: no visible global function definition for
  'as.dist'
mcmc.target.seq: no visible global function definition for 'runif'
phylo.diff: no visible global function definition for 'par'
phylo.diff: no visible global function definition for 'plot'
Undefined global functions or variables:
  as.dist par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.dist", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: 'RUnit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'library' or 'require' call to 'glmnet' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'glmnet' 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running 'testthat.R' [51s]
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)
  > library(dkanr)
  > 
  > 
  > test_check("dkanr")
  -- 1. Error: Connect system is working as expected (@test-connect_system.R#12)  
  Unauthorized (HTTP 401). Failed to connect to DDH.
  1: connect_system(root_url = get_url()) at testthat/test-connect_system.R:12
  2: httr::stop_for_status(out, task = "connect to DDH")
  
  == testthat results  ===========================================================
  OK: 89 SKIPPED: 0 FAILED: 1
  1. Error: Connect system is working as expected (@test-connect_system.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.3Mb
Package suggested but not available for checking: 'asreml'
'library' or 'require' calls to packages already attached by Depends:
  'nlme' 'wgaim'
  Please remove these calls from your code.
'library' or 'require' call to 'asreml' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'ibdreg' 'mgcv' 'nlme' 'qtl' 'wgaim'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'qtl:::adjust.rf.ri'
  See the note in ?`:::` about the use of this operator.
Foreign function call to a different package:
  .C(cfunc, ..., PACKAGE = "qtl")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'rPython'
Package in Depends field not imported from: 'magic'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Warning: no function found corresponding to methods exports from 'DMwR' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  'grid' 'lattice' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing object imported by a ':::' call: 'rpart:::rpconvert'
Unexported objects imported by ':::' calls:
  'rpart:::rpart.branch' 'rpart:::rpartco'
  'rpart:::string.bounding.box'
  See the note in ?`:::` about the use of this operator.
'library' or 'require' call to 'igraph' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
network.modules: no visible global function definition for
  'graph.empty'
network.modules: no visible global function definition for
  'add.vertices'
network.modules: no visible global function definition for 'add.edges'
network.modules: no visible global function definition for 'tkplot'
network.modules: no visible global function definition for 'V'
Undefined global functions or variables:
  V add.edges add.vertices graph.empty tkplot
DNMF: no visible global function definition for 'runif'
NMFpval: no visible global function definition for 'p.adjust'
ndNMF: no visible global function definition for 'runif'
rnk: no visible global function definition for 'write.table'
Undefined global functions or variables:
  p.adjust runif write.table
Consider adding
  importFrom("stats", "p.adjust", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   2.0Mb
Packages which this enhances but not available for checking:
  'gurobi' 'Rmosek'
.info: no visible global function definition for 'packageDescription'
redisWorker: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  flush.console packageDescription
Consider adding
  importFrom("utils", "flush.console", "packageDescription")
to your NAMESPACE file.
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').
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Warning: parse error in file 'testthat/utf-8.R':
2:19: unexpected input
1: # UTF-8 tests that can't be run on Windows CRAN
2: df <- data.frame(ä¸
                     ^
'::' or ':::' import not declared from: 'MASS'
Packages in Depends field not imported from:
  'cluster' 'oro.nifti'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dpmixsim: no visible global function definition for 'runif'
dpmixsim: no visible global function definition for 'clara'
postdpmixciz: no visible global function definition for 'par'
postdpmixciz: no visible global function definition for 'barplot'
postdpmixciz: no visible global function definition for 'dnorm'
postdpmixciz: no visible global function definition for 'hist'
postdpmixciz: no visible global function definition for 'lines'
postdpmixciz: no visible global function definition for 'axis'
postdpmixciz: no visible global function definition for 'dev.cur'
postdpmixciz: no visible global function definition for 'points'
postdpmixciz: no visible global function definition for 'dev.set'
postimgclgrp: no visible global function definition for 'par'
postimgclgrp: no visible global function definition for 'image'
postimgclgrp: no visible global function definition for 'gray'
postimgcomps: no visible global function definition for 'par'
postimgcomps: no visible global function definition for 'image'
postimgcomps: no visible global function definition for 'gray'
postkcluster: no visible global function definition for 'clara'
postkcluster: no visible global function definition for 'par'
postkcluster: no visible global function definition for 'image'
postkcluster: no visible global function definition for 'gray'
readsliceimg: no visible global function definition for 'readNIfTI'
Undefined global functions or variables:
  axis barplot clara dev.cur dev.set dnorm gray hist image lines par
  points readNIfTI runif
Consider adding
  importFrom("grDevices", "dev.cur", "dev.set", "gray")
  importFrom("graphics", "axis", "barplot", "hist", "image", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "runif")
to your NAMESPACE file.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   6.6Mb
File 'DPpackage/libs/i386/DPpackage.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'
File 'DPpackage/libs/x64/DPpackage.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
The following files look like leftovers:
  'drawExpression/visualRefCard/svn-commit.tmp'
Please remove them from your package.
.drawTree: no visible global function definition for 'pdf'
.drawTree: no visible global function definition for 'dev.off'
drawExpression: no visible global function definition for 'plot.new'
Undefined global functions or variables:
  dev.off pdf plot.new
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "plot.new")
to your NAMESPACE file.
DRaWR: no visible global function definition for 'write.table'
DRaWR: no visible global function definition for 'read.table'
DRaWR: no visible global function definition for 'aggregate'
DRaWR: no visible global function definition for 'slot'
Undefined global functions or variables:
  aggregate read.table slot write.table
Consider adding
  importFrom("methods", "slot")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cdfDRM: no visible global function definition for 'tail'
densityDRM: no visible binding for global variable 'density'
drmdel: no visible binding for global variable 'optim'
drmdel: no visible global function definition for 'pchisq'
quantEst: no visible global function definition for 'tail'
quantileCompWald: no visible global function definition for 'pchisq'
quantileCompWald: no visible global function definition for 'p.adjust'
quantileDRM: no visible global function definition for 'tail'
quantileDRM: no visible global function definition for 'density'
Undefined global functions or variables:
  density optim p.adjust pchisq tail
Consider adding
  importFrom("stats", "density", "optim", "p.adjust", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.