installed size is 69.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  67.5Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘dismo’ ‘dplyr’ ‘ecospat’ ‘jsonlite’
  ‘leaflet.extras’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’ ‘sp’
  ‘spThin’ ‘spocc’ ‘zip’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   6.3Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Running examples in ‘warbleR-Ex.R’ failed
The error most likely occurred in:

> ### Name: image_to_wave
> ### Title: Convert images into wave objects
> ### Aliases: image_to_wave
> 
> ### ** Examples
> 
> { 
+  ### create image with text to use in the spectrogram
+  # remove margins of plot
+  par(mar = rep(0, 4))
+  
+  # empty plot
+  plot(0, type='n',axes = FALSE, ann = FALSE, xlim = c(0, 1), ylim = c(0, 1))
+  
+  # text to include
+  text <- " warbleR "
+  
+  # add text
+  text(x = 0.5, y = 0.5, labels = text, cex = 11, font = 1)
+  
+  # save image in temporary directory
+  dev2bitmap(file.path(tempdir(), "temp-img.png"), type = "pngmono", res = 30)
+  
+  # read it 
+   wv <- image_to_wave(file = file.path(tempdir(), "temp-img.png"), plot = TRUE, flim = c(1, 12))
+ 
+  # output wave object
+  # wv
+   
+  ## plot it   
+  # reset margins
+  par(mar = c(5, 4, 4, 2) + 0.1)
+  
+  # plot spectrogram
+  # spectro(wave = wv, scale = FALSE, collevels = seq(-30, 0, 5),
+  # palette = reverse.terrain.colors, ovlp = 90, grid = FALSE, flim = c(2, 11))
+ }
Error in dev2bitmap(file.path(tempdir(), "temp-img.png"), type = "pngmono",  : 
  GhostScript was not found
Execution halted
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Note: found 3133 marked UTF-8 strings
Note: found 4413 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1660 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Package suggested but not available for checking: ‘prepr’
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘here’ ‘rgeos’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘plotly’ ‘shinythemes’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 6738 marked UTF-8 strings
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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.
Note: found 3 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.3Mb
  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 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘ROTS’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.4Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.6Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    bin   4.2Mb
    lib   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 47.1Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘psychTools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    java  34.2Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ChemmineR', 'fmcsR'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggdendro’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/xpose.nlmixr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs      2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 43.1Mb
  sub-directories of 1Mb or more:
    libs  42.7Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘XML’ ‘atom4R’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 47 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 146804 marked UTF-8 strings
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
'LazyData' is specified without a 'data' directory
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    libs  36.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘zdat’
Package suggested but not available for checking: ‘SDMTools’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
Running examples in 'ACEP-Ex.R' failed
The error most likely occurred in:

> ### Name: acep_load_base
> ### Title: Carga bases de datos creadas por el Observatorio.
> ### Aliases: acep_load_base
> ### Keywords: datos
> 
> ### ** Examples
> 
> bd_sismos <- 'https://zenodo.org/record/6835713/files/bd_sismos_mdp.rds?download=1'
> acep_load_base(tag = bd_sismos) |> head()
trying URL 'https://zenodo.org/record/6835713/files/bd_sismos_mdp.rds'
Warning in download.file(url, destfile) :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in download.file(url, destfile) : 
  cannot open URL 'https://zenodo.org/record/6835713/files/bd_sismos_mdp.rds'
Calls: head -> acep_load_base -> download.file
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R  14.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.9Mb
    pictures   2.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.1Mb
Package suggested but not available for checking: 'metaboliteIDmapping'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/ANN2.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    test_v8    2.0Mb
    testdata   2.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.3Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
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'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is 73.2Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs  67.9Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      2.1Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    bin   22.9Mb
    misc   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'asteRiskData'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'ATNr.Rmd' using rmarkdown
--- finished re-building 'ATNr.Rmd'

--- re-building 'model_descriptions.ltx' using tex
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "model_descriptions.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'model_descriptions.ltx' failed with diagnostics:
running 'texi2dvi' on 'model_descriptions.ltx' failed

BibTeX errors:
I couldn't open database file vignette.bib.bib
---line 47 of file model_descriptions.aux
 : \bibdata{vignette.bib
 :                      }
I'm skipping whatever remains of this command
I found no database files---while reading file model_descriptions.aux

--- failed re-building 'model_descriptions.ltx'

SUMMARY: processing the following file failed:
  'model_descriptions.ltx'

Error: Vignette re-building failed.
Execution halted
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 56.6Mb
  sub-directories of 1Mb or more:
    libs  55.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

  Natural language support but running in an English locale

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

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

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(badger)
  > 
  > test_check("badger")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ]
  
  == Failed tests ================================================================
  -- Error (test-badges.R:90:3): Other badges output as expected -----------------
  Error in `file(con, "r")`: cannot open the connection
  Backtrace:
      x
   1. +-testthat::expect_equal(...) at test-badges.R:90:2
   2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
   3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
   4. \-badger::badge_sci_citation(...)
   5.   +-base::suppressWarnings(readLines(url))
   6.   | \-base::withCallingHandlers(...)
   7.   \-base::readLines(url)
   8.     \-base::file(con, "r")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'baffle.Rmd' using rmarkdown
Quitting from lines 88-95 (baffle.Rmd) 
Error: processing vignette 'baffle.Rmd' failed with diagnostics:
unused arguments (title.font = 2, title.cex = 1.5)
--- failed re-building 'baffle.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
NB: this package is only installed for sub-architecture 'x64'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/bayesbr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/bayesdfa.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   2.7Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
GNU make is a SystemRequirements.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.7Mb
GNU make is a SystemRequirements.
NeedsCompilation field should likely be 'yes'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.1Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/bayesnec.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.8Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.3Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/beanz.Rcheck/00install.out' for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   5.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    help   1.1Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
installed size is 149.8Mb
  sub-directories of 1Mb or more:
    include  148.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.9Mb
    libs      2.2Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
GNU make is a SystemRequirements.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   2.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.7Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      2.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'blandr-Ex.R' failed
The error most likely occurred in:

> ### Name: blandr.dataset.fibre
> ### Title: Function to load D'arbela mean velocity of circumferential fibre
> ###   shortening dataset from internet
> ### Aliases: blandr.dataset.fibre
> 
> ### ** Examples
> 
> blandr.dataset.fibre()
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: blandr.dataset.fibre -> readLines -> file
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: 'cmdstanr'
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
'::' or ':::' import not declared from: 'StochBlockTest'
'library' or 'require' call not declared from: 'StochBlockTest'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
GNU make is a SystemRequirements.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   7.9Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
installed size is 67.7Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    lib      58.4Mb
GNU make is a SystemRequirements.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.4Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Package suggested but not available for checking: 'cmdstanr'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   3.6Mb
Package suggested but not available for checking: 'glmmADMB'
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.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    help   1.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    fonts   3.1Mb
    lib     4.6Mb
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/BuyseTest.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/CA3variants.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'simstudy_survival.Rnw' using Sweave
Loading required package: mice

Attaching package: 'mice'

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

    filter

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

    cbind, rbind


Error: processing vignette 'simstudy_survival.Rnw' failed with diagnostics:
 chunk 7 
Error in loadNamespace(x) : there is no package called 'ranger'

--- failed re-building 'simstudy_survival.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'ReGenesees'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc        2.1Mb
    pictures   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
'LazyData' is specified without a 'data' directory
Running examples in 'caroline-Ex.R' failed
The error most likely occurred in:

> ### Name: volins
> ### Title: Plot a Series of Vioplot Violins
> ### Aliases: violins
> 
> ### ** Examples
> 
> 
> n <- rnorm(130, 10, 3)
> p <- rpois(110, 4)
> u <- runif(300, 0, 20)
> l <- rlnorm(130, log(2))
> g <- rgamma(140, 3)
> e <- rexp(160)
> 
> violins(list(e=e, p=p,u=u,n=n,l=l,g=g), ylim=c(0,20),
+          col=c('purple','lightblue','lightgreen','red','orange','yellow'),
+          stats=TRUE)
Loading required namespace: sm
Failed with error:  'there is no package called 'sm''
Loading required namespace: MASS
Error in loadNamespace(x) : there is no package called 'sm'
Calls: violins ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.1Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    doc  37.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   1.1Mb
    libs      2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running examples in 'cbsodataR-Ex.R' failed
The error most likely occurred in:

> ### Name: cbs_get_catalogs
> ### Title: Retrieves the possible catalog values that can be used for
> ###   retrieving data
> ### Aliases: cbs_get_catalogs
> 
> ### ** Examples
> 
> catalogs <- cbs_get_catalogs()
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Warning: Failing: http://opendata.cbs.nl/ODataCatalog/Tables?$format=json
Retrying...
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: cbs_get_catalogs ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/CDatanet.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.4Mb
    libs   3.4Mb
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/ChemoSpecUtils.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'countreg'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char ï»¿ (U+FEFF)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char ï»¿ (U+FEFF)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'entab'
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.5Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'cmfrec-Ex.R' failed
The error most likely occurred in:

> ### Name: CMF.from.model.matrices
> ### Title: Create a CMF model object from fitted matrices
> ### Aliases: CMF.from.model.matrices
> 
> ### ** Examples
> 
> ### Example 'adopting' a model from 'recosystem'
> library(cmfrec)
> library(recosystem)
> library(recommenderlab)
Loading required package: Matrix
Loading required package: arules

Attaching package: 'arules'

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

    abbreviate, write

Loading required package: proxy

Attaching package: 'proxy'

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

    as.matrix

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

    as.dist, dist

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

    as.matrix

Loading required package: registry
> library(MatrixExtra)
Error: package 'MatrixExtra' is not installed for 'arch = i386'
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/CNVRG.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/CohortPlat.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: unable to re-encode 'supsc.R' line 117
See 'd:/Rcompile/CRANpkg/local/4.1/common.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/commonsMath.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ProData'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.3Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.6Mb
    libs   5.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   5.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   7.2Mb
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 '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 '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 '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 '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 quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'robustbase'
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.0Mb
    libs   2.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    demos         4.3Mb
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'doMC'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    deps  10.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    deps   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'datafaker_workflow.Rmd' using rmarkdown
--- finished re-building 'datafaker_workflow.Rmd'

--- re-building 'extra_parameters.Rmd' using rmarkdown
--- finished re-building 'extra_parameters.Rmd'

--- re-building 'main.Rmd' using rmarkdown
Error: processing vignette 'main.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'main.Rmd'

--- re-building 'schema_structure.Rmd' using rmarkdown
--- finished re-building 'schema_structure.Rmd'

--- re-building 'simulation_methods.Rmd' using rmarkdown
--- finished re-building 'simulation_methods.Rmd'

--- re-building 'simulation_options.Rmd' using rmarkdown
--- finished re-building 'simulation_options.Rmd'

--- re-building 'structure_from_db.Rmd' using rmarkdown
--- finished re-building 'structure_from_db.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dblog'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'dbnR-Ex.R' failed
The error most likely occurred in:

> ### Name: calc_mu
> ### Title: Calculate the mu vector of means of a Gaussian linear network.
> ###   Front end of a C++ function.
> ### Aliases: calc_mu
> 
> ### ** Examples
> 
> dt_train <- dbnR::motor[200:2500]
> net <- bnlearn::mmhc(dt_train)
> fit <- bnlearn::bn.fit(net, dt_train, method = "mle")
Error in check.fitting.method(method, data) : 
  parameter estimator 'mle' may only be used with discrete data.
Calls: <Anonymous> -> check.fitting.method
Execution halted
Running examples in 'dbnR-Ex.R' failed
The error most likely occurred in:

> ### Name: calc_mu
> ### Title: Calculate the mu vector of means of a Gaussian linear network.
> ###   Front end of a C++ function.
> ### Aliases: calc_mu
> 
> ### ** Examples
> 
> dt_train <- dbnR::motor[200:2500]
> net <- bnlearn::mmhc(dt_train)
> fit <- bnlearn::bn.fit(net, dt_train, method = "mle")
Error in check.fitting.method(method, data) : 
  parameter estimator 'mle' may only be used with discrete data.
Calls: <Anonymous> -> check.fitting.method
Execution halted
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
as(<dsCMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "generalMatrix") instead
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11352 (sockconn)
Execution halted
Package suggested but not available for checking: 'doMC'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'spelling.R' [0s]
  Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(deepdep)
  > 
  > test_check("deepdep")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 45 ]
  
  == Skipped tests ===============================================================
  * On CRAN (2)
  
  == Failed tests ================================================================
  -- Error (test-deepdep.R:32:3): obtaining Bioc dependencies returns objects of correct types --
  Error in `value[[3L]](cond)`: les is not available neither on CRAN nor on Bioconductor
  Backtrace:
      x
   1. +-vcr::use_cassette(...) at test-deepdep.R:32:2
   2. | \-cassette$call_block(...)
   3. \-deepdep (local) deepdep_wrapped(...) at test-deepdep.R:33:4
   4.   \-base::tryCatch(...) at test-deepdep.R:3:2
   5.     \-base (local) tryCatchList(expr, classes, parentenv, handlers)
   6.       \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7.         \-value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 45 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Warning: found non-ASCII strings
  'SRP05673: monocyte derived macrophages. none vs bacillus Calmette-Gu<c3><83><c2><a9>rin' in object 'DEET_example_data'
  'treated with: 100 nM 17<c3><9f>-estradiol + 25 ng/mL TNFa for 40min:3' in object 'DEET_example_data'
  'treated with: 100 nM 17<c3><9f>-estradiol (E2) for 40min:3' in object 'DEET_example_data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in 'demcon-Ex.R' failed
The error most likely occurred in:

> ### Name: get_cce
> ### Title: Retrieve Chronology of Constitutional Events Dataset
> ### Aliases: get_cce
> 
> ### ** Examples
> 
> 
> cce<-get_cce(del_file=TRUE, write_out = FALSE)
trying URL 'https://comparativeconstitutionsproject.org/data/ccpcce_v1_3.zip'
Warning in utils::download.file(cce_url, file.path(tempdir(), "ccpcce_v1_3.zip")) :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in utils::download.file(cce_url, file.path(tempdir(), "ccpcce_v1_3.zip")) : 
  cannot open URL 'https://comparativeconstitutionsproject.org/data/ccpcce_v1_3.zip'
Calls: get_cce -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
Package suggested but not available for checking: 'Rdonlp2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.5Mb
    libs   2.4Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ## Not run: 
> ##D 
> ##D source_url("https://gist.github.com/hadley/6872663/raw/hi.r")
> ##D 
> ##D # With a hash, to make sure the remote file hasn't changed
> ##D source_url("https://gist.github.com/hadley/6872663/raw/hi.r",
> ##D   sha1 = "54f1db27e60bb7e0486d785604909b49e8fef9f9")
> ##D 
> ##D # With a truncated hash
> ##D source_url("https://gist.github.com/hadley/6872663/raw/hi.r",
> ##D   sha1 = "54f1db27e60")
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.35 0.14 3.49 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
as(<dsCMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "generalMatrix") instead
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

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

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11326 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11326 (sockconn)
Execution halted
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
as(<dsCMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "generalMatrix") instead
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

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

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11506 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11506 (sockconn)
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' calls not declared from:
  'MASS' 'Matrix' 'NNMF' 'RANN' 'RSpectra' 'c' 'coRanking' 'ggplot'
  'igraph' 'loe' 'scales' 'tidyr'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'library' or 'require' calls not declared from:
  'keras' 'reticulate' 'tensorflow' 'vegan'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Package suggested but not available for checking: 'BOLTSSIRR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    include  15.5Mb
    libs      1.8Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   3.4Mb
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/doebioresearch.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Package suggested but not available for checking: 'dsBaseClient'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.5Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 40.0Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   1.2Mb
Running examples in 'dynr-Ex.R' failed
The error most likely occurred in:

> ### Name: coef.dynrModel
> ### Title: Extract fitted parameters from a dynrCook Object
> ### Aliases: coef.dynrCook coef.dynrModel coef<- coef<-.dynrModel
> 
> ### ** Examples
> 
> # Create a minimal cooked model called 'cook'
> require(dynr)
> 
> meas <- prep.measurement(
+ 	values.load=matrix(c(1, 0), 1, 2),
+ 	params.load=matrix(c('fixed', 'fixed'), 1, 2),
+ 	state.names=c("Position","Velocity"),
+ 	obs.names=c("y1"))
> 
> ecov <- prep.noise(
+ 	values.latent=diag(c(0, 1), 2),
+ 	params.latent=diag(c('fixed', 'dnoise'), 2),
+ 	values.observed=diag(1.5, 1),
+ 	params.observed=diag('mnoise', 1))
> 
> initial <- prep.initial(
+ 	values.inistate=c(0, 1),
+ 	params.inistate=c('inipos', 'fixed'),
+ 	values.inicov=diag(1, 2),
+ 	params.inicov=diag('fixed', 2))
> 
> dynamics <- prep.matrixDynamics(
+ 	values.dyn=matrix(c(0, -0.1, 1, -0.2), 2, 2),
+ 	params.dyn=matrix(c('fixed', 'spring', 'fixed', 'friction'), 2, 2),
+ 	isContinuousTime=TRUE)
> 
> data(Oscillator)
> data <- dynr.data(Oscillator, id="id", time="times", observed="y1")
> 
> model <- dynr.model(dynamics=dynamics, measurement=meas,
+ 	noise=ecov, initial=initial, data=data)
> 
> cook <- dynr.cook(model,
+ 	verbose=FALSE, optimization_flag=FALSE, hessian_flag=FALSE)
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'D:/temp/RtmpAnKP/file106584c5b6663.c': No such file or directory
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: dynr.cook ... .C2funcaddress -> CompileCode -> write -> cat -> file
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   2.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    bin       7.1Mb
    extdata   1.7Mb
    libs      2.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Title: Trim and Format Address Information
> ### Aliases: trim_address
> 
> ### ** Examples
> 
> addr_string <- " 2 Dept of Urology, Feinberg School of Medicine," 
> addr_string <- paste(addr_string, "Chicago, US; Dept of Mol Bio as well...")
> print(addr_string)
[1] " 2 Dept of Urology, Feinberg School of Medicine, Chicago, US; Dept of Mol Bio as well..."
> print(trim_address(addr = addr_string))
[1] "Dept of Urology, Feinberg School of Medicine, Chicago, US"
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.9 0.78 486.97 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'econet.tex' using tex
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "econet.tex" --max-iterations=20 -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'econet.tex' failed with diagnostics:
running 'texi2dvi' on 'econet.tex' failed

LaTeX errors:
! LaTeX Error: File `orcidlink.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)


--- failed re-building 'econet.tex'

SUMMARY: processing the following file failed:
  'econet.tex'

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'eggCountsExtra'
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'Introduction_to_eHDPrep.Rmd' using rmarkdown
Warning: Removed 12 rows containing missing values (geom_point).
Warning: Removed 12 rows containing missing values (geom_label).
! Package pdftex.def Error: File `./images/Figure\unhbox \voidb@x \penalty \@M 
\hskip \z@skip \T1\textunderscore \discretionary {-}{}{}\penalty \@M \hskip \z@
skip 1.png' not found.

Error: processing vignette 'Introduction_to_eHDPrep.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/eHDPrep.Rcheck/vign_test/eHDPrep/vignettes/Introduction_to_eHDPrep.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Introduction_to_eHDPrep.log for more info.
--- failed re-building 'Introduction_to_eHDPrep.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'epidict'
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.0Mb
Package suggested but not available for checking: 'EpiSoon'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/EpiNow2.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    java   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    libs      2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Package suggested but not available for checking: 'ExactData'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'exuberdata'
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'fame/R/windows/zzz.R':
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section 'Good practice' in '?.onAttach'.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      3.3Mb
    doc    1.0Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'FAMoS-EvaluationFunctions.Rmd' using rmarkdown
Error: processing vignette 'FAMoS-EvaluationFunctions.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'FAMoS-EvaluationFunctions.Rmd'

Warning messages:
1: In stats::optim(par = opt.par, fn = combine.and.fit, par.names = names(parms),  :
  one-dimensional optimization by Nelder-Mead is unreliable:
use "Brent" or optimize() directly
2: In stats::optim(par = opt.par, fn = combine.and.fit, par.names = names(parms),  :
  one-dimensional optimization by Nelder-Mead is unreliable:
use "Brent" or optimize() directly
3: In stats::optim(par = opt.par, fn = combine.and.fit, par.names = names(parms),  :
  one-dimensional optimization by Nelder-Mead is unreliable:
use "Brent" or optimize() directly
4: In stats::optim(par = opt.par, fn = combine.and.fit, par.names = names(parms),  :
  one-dimensional optimization by Nelder-Mead is unreliable:
use "Brent" or optimize() directly
--- re-building 'FAMoS-Examples.Rmd' using rmarkdown
Error: processing vignette 'FAMoS-Examples.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'FAMoS-Examples.Rmd'

SUMMARY: processing the following files failed:
  'FAMoS-EvaluationFunctions.Rmd' 'FAMoS-Examples.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     2.5Mb
Package suggested but not available for checking: 'coxKM'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'fastmatch/libs/i386/fastmatch.dll':
  Found non-API call to R: 'match5'
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    Rcgi      2.8Mb
    cgi-bin   2.7Mb
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Undefined global functions or variables:
  init run
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   2.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.9Mb
Unexported objects imported by ':::' calls:
  'fdapace:::GCVLwls1D1' 'fdapace:::GetSmoothedMeanCurve'
  'fdapace:::HandleNumericsAndNAN' 'fdapace:::interp2lin'
  See the note in ?`:::` about the use of this operator.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.0Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  fgsg.h:96:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:202:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:347:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:460:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:516:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:636:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:717:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:852:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:996:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.1/FGSG.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      2.2Mb
Package suggested but not available for checking: 'MicrobeDS'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/fido.Rcheck/00install.out' for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R         4.3Mb
    doc       2.2Mb
    extdata   2.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required and available but unsuitable versions: 'strex', 'stringi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    lib    5.7Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fivethirtyeightdata'
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.6Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.2Mb
  sub-directories of 1Mb or more:
    libs  37.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    9.0Mb
    libs   2.0Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/fm.index.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.4Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
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 27.6Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.5Mb
    libs  20.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'fuzzyRankTests/libs/i386/fuzzyRankTests.dll':
  Found non-API calls to R: 'signrank_free', 'wilcox_free'
File 'fuzzyRankTests/libs/x64/fuzzyRankTests.dll':
  Found non-API calls to R: 'signrank_free', 'wilcox_free'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    bin   8.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is 47.4Mb
  sub-directories of 1Mb or more:
    doc   44.4Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'tools:::.Rd_get_argument_names' 'tools:::RdTags' 'tools:::fetchRdDB'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 112.1Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    gdal     2.2Mb
    libs    98.0Mb
    proj     8.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.8Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.2Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'genderdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    1.9Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'geomarocdata'
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R         9.4Mb
    extdata   1.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'getwiki-Ex.R' failed
The error most likely occurred in:

> ### Name: get_wiki
> ### Title: Get the Text of a Wikipedia Article
> ### Aliases: get_wiki
> 
> ### ** Examples
> 
> get_wiki("United States")
Error: Required package curl not found. Please run: install.packages('curl')
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       5.2Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ggOceanMapsData'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'ggpie.Rmd' using rmarkdown
Error: processing vignette 'ggpie.Rmd' failed with diagnostics:
there is no package called 'prettydoc'
--- failed re-building 'ggpie.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.3Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.3Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    1.8Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/glmmfields.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs           22.1Mb
    test_data       2.2Mb
    vignette_data   1.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Error(s) in re-building vignettes:
--- re-building 'intro.rmd' using rmarkdown
trying URL 'https://web.stanford.edu/~hastie/glmnet/glmnetData/Leukemia.RData'
Quitting from lines 167-173 (intro.rmd) 
Error: processing vignette 'intro.rmd' failed with diagnostics:
cannot open URL 'https://web.stanford.edu/~hastie/glmnet/glmnetData/Leukemia.RData'
--- failed re-building 'intro.rmd'

SUMMARY: processing the following file failed:
  'intro.rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'glmtlp.Rmd' using rmarkdown
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

Error: processing vignette 'glmtlp.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/glmtlp.Rcheck/vign_test/glmtlp/vignettes/glmtlp.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See glmtlp.log for more info.
--- failed re-building 'glmtlp.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cplexAPI'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
3                  description_url  FALSE
4           description_bugreports  FALSE
5          lintr_assignment_linter   TRUE
6         lintr_line_length_linter   TRUE
7  lintr_trailing_semicolon_linter  FALSE
8       lintr_attach_detach_linter   TRUE
9               lintr_setwd_linter   TRUE
10             lintr_sapply_linter   TRUE
11    lintr_library_require_linter   TRUE
12                lintr_seq_linter   TRUE
13    no_import_package_as_a_whole  FALSE
14               no_export_pattern   TRUE
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  2 0.22 2.2 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R   6.5Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'getting-started.Rmd' using rmarkdown
Quitting from lines 27-34 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
File not found; If you want to access non-local files directly, please install the RCurl package!
--- failed re-building 'getting-started.Rmd'

SUMMARY: processing the following file failed:
  'getting-started.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
Package suggested but not available for checking: 'doMC'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    2.6Mb
    libs   2.0Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: unable to re-encode 'guiplotServer.R' lines 318, 319
See 'd:/Rcompile/CRANpkg/local/4.1/guiplot.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.5Mb
    libs      2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 182.0Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    java  179.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs    2.0Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    HaDeX   3.9Mb
    doc     4.0Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hazer)
  > 
  > test_check("hazer")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  
  == Failed tests ================================================================
  -- Failure (testall.R:22:3): test the haze -------------------------------------
  floor(h$haze * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 225, 224).
  1/1 mismatches
  [1] 224 - 225 == -1
  -- Failure (testall.R:23:3): test the haze -------------------------------------
  floor(h$A0 * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 710, 712).
  1/1 mismatches
  [1] 712 - 710 == 2
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'hedgehog.Rmd' using rmarkdown
Loading required package: testthat
Error: processing vignette 'hedgehog.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'hedgehog.Rmd'

--- re-building 'state-machines.Rmd' using rmarkdown
Loading required package: testthat
Error: processing vignette 'state-machines.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'state-machines.Rmd'

SUMMARY: processing the following files failed:
  'hedgehog.Rmd' 'state-machines.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
    libs      3.9Mb
':::' call which should be '::': 'ggplot2:::guide_axis'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'ggplot2:::build_guides' 'ggplot2:::scales_list'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'FGN'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   2.3Mb
    libs   2.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
Package suggested but not available for checking: 'ROI.plugin.mosek'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.5Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
Running examples in 'htm2txt-Ex.R' failed
The error most likely occurred in:

> ### Name: browse
> ### Title: Display simple plain texts in a web page at a certain URL
> ### Aliases: browse
> 
> ### ** Examples
> 
> browse("https://www.wikipedia.org/")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: browse ... htm2txt -> as.vector -> unlist -> paste -> readLines -> file
Execution halted
Running examples in 'htmcglm-Ex.R' failed
The error most likely occurred in:

> ### Name: mc_anova_I
> ### Title: ANOVA type I table for mcglm objects via Wald test.
> ### Aliases: mc_anova_I
> 
> ### ** Examples
> 
> 
> library(mcglm)
----------------------------------------------------------------------
  mcglm: Multivariate Covariance Generalized Linear Models

  For support, collaboration or bug report, visit: 
    http://mcglm.leg.ufpr.br/

  mcglm version 0.7.0 (build on 2021-07-07) is now loaded.
----------------------------------------------------------------------
> library(Matrix)
> library(htmcglm)
> 
> data("soya", package = "mcglm")
> 
> form.grain <- grain ~ water * pot
> form.seed <- seeds ~ water * pot
> 
> soya$viablepeasP <- soya$viablepeas / soya$totalpeas
> form.peas <- viablepeasP ~ water * pot
> 
> Z0 <- mc_id(soya)
> Z1 <- mc_mixed(~0 + factor(block), data = soya)
> 
> fit_joint <- mcglm(linear_pred = c(form.grain,
+                                    form.seed,
+                                    form.peas),
+                    matrix_pred = list(c(Z0, Z1),
+                                       c(Z0, Z1),
+                                       c(Z0, Z1)),
+                    link = c("identity",
+                             "log",
+                             "logit"),
+                    variance = c("constant",
+                                 "tweedie",
+                                 "binomialP"),
+                    Ntrial = list(NULL,
+                                  NULL,
+                                  soya$totalpeas),
+                    power_fixed = c(TRUE,TRUE,TRUE),
+                    data = soya)
Automatic initial values selected. 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'forceSymmetric' for signature '"dgCMatrix", "logical"'
Error: $ operator is invalid for atomic vectors
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'design-principles.Rmd' using rmarkdown
--- finished re-building 'design-principles.Rmd'

--- re-building 'huxreg.Rmd' using rmarkdown
--- finished re-building 'huxreg.Rmd'

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'huxtable'

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

    add_rownames

! Missing \endcsname inserted.
<to be read again> 
                   \egroup 
l.151 \begin
            {threeparttable} 

Error: processing vignette 'huxtable.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/huxtable.Rcheck/vign_test/huxtable/vignettes/huxtable.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See huxtable.log for more info.
--- failed re-building 'huxtable.Rmd'

--- re-building 'themes.Rhtml' using knitr
--- finished re-building 'themes.Rhtml'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    exdata   6.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(IDConverter)
  > 
  > test_check("IDConverter")
  trying URL 'https://zenodo.org/record/6342397/files/icgc.rda'
  trying URL 'https://zenodo.org/record/6342397/files/pcawg_full.rda'
  trying URL 'https://zenodo.org/record/6342397/files/pcawg_full.rda'
  trying URL 'https://zenodo.org/record/6342397/files/pcawg_full.rda'
  trying URL 'https://zenodo.org/record/6342397/files/pcawg_full.rda'
  trying URL 'https://zenodo.org/record/6342397/files/icgc.rda'
  trying URL 'https://zenodo.org/record/6342397/files/tcga.rda'
  trying URL 'https://zenodo.org/record/6342397/files/pcawg_full.rda'
  [ FAIL 4 | WARN 32 | SKIP 0 | PASS 4 ]
  
  == Failed tests ================================================================
  -- Failure (test-roxytest-testexamples-convert_icgc.R:13:3): Function convert_icgc() @ L25 --
  `convert_pcawg("SA170678")` did not throw an error.
  -- Failure (test-roxytest-testexamples-convert_pcawg.R:19:3): Function convert_pcawg() @ L38 --
  `convert_pcawg("SA5213")` did not throw an error.
  -- Failure (test-roxytest-testexamples-convert_pcawg.R:21:3): Function convert_pcawg() @ L38 --
  `convert_icgc("SP1677", from = "icgc_specimen_id", to = "xx")` did not throw an error.
  -- Failure (test-roxytest-testexamples-convert_tcga.R:13:3): Function convert_tcga() @ L24 --
  `convert_pcawg("TCGA-02-0001-10A-01W-0188-10")` did not throw an error.
  
  [ FAIL 4 | WARN 32 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/IFAA.Rcheck/00install.out' for details.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> model <- univariatePrior("logit-norm", "x1", -1)
> model$priorParam$values[1,1] <- -.6
> model <- mxRun(model)
Running univariatePrior with 1 parameter
> model$output$fit
[1] 0.4515827
> model$output$gradient
x1 
 0 
> model$output$hessian
   x1
x1  8
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  8.3 0.32 8.67 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.2Mb
    libs  13.4Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.7Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    dlib-19.20   8.9Mb
    libs         2.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     16.0Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs   19.3Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.6Mb
    libs   2.0Mb
Running examples in 'immunarch-Ex.R' failed
The error most likely occurred in:

> ### Name: repLoad
> ### Title: Load immune repertoire files into the R workspace
> ### Aliases: repLoad
> 
> ### ** Examples
> 
> # To load the data from a single file (note that you don't need to specify the data format):
> file_path <- paste0(system.file(package = "immunarch"), "/extdata/io/Sample1.tsv.gz")
> immdata <- repLoad(file_path)

== Step 1/3: loading repertoire files... ==

Processing "<initial>" ...
  -- [1/1] Parsing "D:/temp/RtmpULq4sE/RLIBS_b38460a31c6c/immunarch/extdata/io/Sample1.tsv.gz" -- immunarch

== Step 2/3: checking metadata files and merging files... ==

Processing "<initial>" ...
  -- Metadata file not found; creating a dummy metadata...

== Step 3/3: processing paired chain data... ==

Done!

> 
> # Suppose you have a following structure in your folder:
> # >_ ls
> # immunoseq1.txt
> # immunoseq2.txt
> # immunoseq3.txt
> # metadata.txt
> 
> # To load the whole folder with every file in it type:
> file_path <- paste0(system.file(package = "immunarch"), "/extdata/io/")
> immdata <- repLoad(file_path)

== Step 1/3: loading repertoire files... ==

Error in .split_to_batches(.path, "<initial>") : 
  Input file or directory not found: D:/temp/RtmpULq4sE/RLIBS_b38460a31c6c/immunarch/extdata/io/
Calls: repLoad -> .split_to_batches
Execution halted
Running examples in 'immunarch-Ex.R' failed
The error most likely occurred in:

> ### Name: repLoad
> ### Title: Load immune repertoire files into the R workspace
> ### Aliases: repLoad
> 
> ### ** Examples
> 
> # To load the data from a single file (note that you don't need to specify the data format):
> file_path <- paste0(system.file(package = "immunarch"), "/extdata/io/Sample1.tsv.gz")
> immdata <- repLoad(file_path)

== Step 1/3: loading repertoire files... ==

Processing "<initial>" ...
  -- [1/1] Parsing "D:/temp/RtmpULq4sE/RLIBS_b38460a31c6c/immunarch/extdata/io/Sample1.tsv.gz" -- immunarch

== Step 2/3: checking metadata files and merging files... ==

Processing "<initial>" ...
  -- Metadata file not found; creating a dummy metadata...

== Step 3/3: processing paired chain data... ==

Done!

> 
> # Suppose you have a following structure in your folder:
> # >_ ls
> # immunoseq1.txt
> # immunoseq2.txt
> # immunoseq3.txt
> # metadata.txt
> 
> # To load the whole folder with every file in it type:
> file_path <- paste0(system.file(package = "immunarch"), "/extdata/io/")
> immdata <- repLoad(file_path)

== Step 1/3: loading repertoire files... ==

Error in .split_to_batches(.path, "<initial>") : 
  Input file or directory not found: D:/temp/RtmpULq4sE/RLIBS_b38460a31c6c/immunarch/extdata/io/
Calls: repLoad -> .split_to_batches
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'accdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.1Mb
    libs   2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
GNU make is a SystemRequirements.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field should be the URL of a single webpage
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
File 'iotools/libs/i386/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R  11.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   5.3Mb
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.2Mb
    data   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'locClass'
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           9.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'janitor.Rmd' using rmarkdown

Attaching package: 'janitor'

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

    chisq.test, fisher.test

pandoc.exe: Unknown extension: gfm_auto_identifiers
Error: processing vignette 'janitor.Rmd' failed with diagnostics:
pandoc document conversion failed with error 7
--- failed re-building 'janitor.Rmd'

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Error: processing vignette 'tabyls.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'tabyls.Rmd'

SUMMARY: processing the following files failed:
  'janitor.Rmd' 'tabyls.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'JFE-Ex.R' failed
The error most likely occurred in:

> ### Name: getFed
> ### Title: Download financial and economic time series data from the Fed
> ### Aliases: getFed
> 
> ### ** Examples
> 
> 
> getFed(var.name="UNRATE")$data
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(file, "rt") : cannot open the connection
Calls: getFed -> read.csv -> read.table -> file
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    i18n   4.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'Kmedians-Ex.R' failed
The error most likely occurred in:

> ### Name: Kmeans
> ### Title: Kmeans
> ### Aliases: Kmeans
> ### Keywords: K-means
> 
> ### ** Examples
> 
> n <- 500
> K <- 3
> pcont <- 0.2
> ech <- gen_K(n=n,K=K,pcont=pcont)
> X <-ech$X
> res <- Kmeans(X,par=FALSE)
Error in library(p, character.only = TRUE) : 
  there is no package called 'dplyr'
Calls: Kmeans -> %do% -> <Anonymous> -> library
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs             2.4Mb
    shiny-landsepi   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   8.8Mb
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/leidenAlg.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Package unavailable to check Rd xrefs: 'doMC'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    doc       1.0Mb
    extdata   1.1Mb
    libs      3.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   2.1Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Codoc mismatches from documentation object 'gloss_example':
gloss_example
  Code: function(transliteration, glosses, free_translation = "",
                 comment = "", annotation = NULL, grammaticality =
                 NULL, audio_path = NULL, audio_label = "<U+266A>",
                 video_path = NULL, video_width = 320, video_height =
                 240, line_length = 70, italic_transliteration = TRUE,
                 drop_transliteration = FALSE, intext = FALSE,
                 write_to_db = TRUE)
  Docs: function(transliteration, glosses, free_translation = "",
                 comment = "", annotation = NULL, grammaticality =
                 NULL, audio_path = NULL, audio_label = "<U+266A>",
                 video_path = NULL, video_width = 320, video_height =
                 240, line_length = 70, italic_transliteration = TRUE,
                 drop_transliteration = FALSE, intext = FALSE,
                 write_to_db = TRUE)
  Mismatches in argument default values:
    Name: 'audio_label' Code: "<U+266A>" Docs: "<U+266A>"
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.0Mb
    libs       2.7Mb
    testdata   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/container/detail/copy_move_algo.hpp:184:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/container/detail/copy_move_algo.hpp:199:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/container/detail/copy_move_algo.hpp:912:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.1/lolog.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/lrstat.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/LST.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs   2.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
Found the following significant warnings:
  lxb.c:62:21: warning: '%d' directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.1/lxb.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(madrat)
  Loading required package: magclass
  > 
  > test_check("madrat")
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 386 ]
  
  == Skipped tests ===============================================================
  * On CRAN (6)
  * reshape2 cannot be loaded (1)
  
  == Failed tests ================================================================
  -- Failure (test-config.R:3:3): cache folder can be set properly ---------------
  getwd() not identical to getConfig("cachefolder").
  1/1 mismatches
  x[1]: "d:/Rcompile/CRANpkg/local/4.1/madrat.Rcheck/tests/testthat"
  y[1]: "d:/RCompile/CRANpkg/local/4.1/madrat.Rcheck/tests/testthat"
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 386 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Package suggested but not available for checking: 'doMC'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   2.9Mb
installed size is 77.5Mb
  sub-directories of 1Mb or more:
    doc    6.6Mb
    libs  70.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs          6.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
+     init_portfolio(
+       years = 2000:2020,
+       outdir = file.path(temp_loc, "res"),
+       tmpdir = tempdir(),
+       add_resources = FALSE,
+       cores = 1,
+       verbose = FALSE
+     ) %>%
+     get_resources("nasa_srtm") %>%
+     calc_indicators("tri", stats_tri = c("mean", "median", "sd", "var"), engine = "extract") %>%
+     tidyr::unnest(tri)))
+ }
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  25.38 1.34 30.19 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs       2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'flashr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   3.2Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(Matrix.utils)
  Loading required package: Matrix
  > 
  > test_check("Matrix.utils")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 16 ]
  
  == Failed tests ================================================================
  -- Failure (tests.R:43:3): merge.Matrix can handle mixed types -----------------
  `merge.Matrix(...)` did not throw an error.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 16 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cplexAPI'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   3.0Mb
Running examples in 'mcglm-Ex.R' failed
The error most likely occurred in:

> ### Name: Hunting
> ### Title: Hunting in Pico Basile, Bioko Island, Equatorial Guinea.
> ### Aliases: Hunting
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(mcglm)
> library(Matrix)
> data(Hunting, package="mcglm")
> formu <- OT ~ METHOD*ALT + SEX + ALT*poly(MONTH, 4)
> Z0 <- mc_id(Hunting)
> Z1 <- mc_mixed(~0 + HUNTER.MONTH, data = Hunting)
> fit <- mcglm(linear_pred = c(formu), matrix_pred = list(c(Z0, Z1)),
+             link = c("log"), variance = c("poisson_tweedie"),
+             power_fixed = c(FALSE),
+             control_algorithm = list(max_iter = 100),
+             offset = list(log(Hunting$OFFSET)), data = Hunting)
Automatic initial values selected. 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'forceSymmetric' for signature '"dgCMatrix", "logical"'
Error: $ operator is invalid for atomic vectors
Execution halted
Running examples in 'mcglm-Ex.R' failed
The error most likely occurred in:

> ### Name: Hunting
> ### Title: Hunting in Pico Basile, Bioko Island, Equatorial Guinea.
> ### Aliases: Hunting
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(mcglm)
> library(Matrix)
> data(Hunting, package="mcglm")
> formu <- OT ~ METHOD*ALT + SEX + ALT*poly(MONTH, 4)
> Z0 <- mc_id(Hunting)
> Z1 <- mc_mixed(~0 + HUNTER.MONTH, data = Hunting)
> fit <- mcglm(linear_pred = c(formu), matrix_pred = list(c(Z0, Z1)),
+             link = c("log"), variance = c("poisson_tweedie"),
+             power_fixed = c(FALSE),
+             control_algorithm = list(max_iter = 100),
+             offset = list(log(Hunting$OFFSET)), data = Hunting)
Automatic initial values selected. 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'forceSymmetric' for signature '"dgCMatrix", "logical"'
Error: $ operator is invalid for atomic vectors
Execution halted
Error(s) in re-building vignettes:
--- re-building 'GLMExamples.Rmd' using rmarkdown
Loading required package: mcglm
----------------------------------------------------------------------
  mcglm: Multivariate Covariance Generalized Linear Models

  For support, collaboration or bug report, visit: 
    http://mcglm.leg.ufpr.br/

  mcglm version 0.7.0 (build on 2021-07-07) is now loaded.
----------------------------------------------------------------------
Loading required package: Matrix
Quitting from lines 67-77 (GLMExamples.Rmd) 
Error: processing vignette 'GLMExamples.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building 'GLMExamples.Rmd'

--- re-building 'UniModels.Rmd' using rmarkdown
Loading required package: mcglm
----------------------------------------------------------------------
  mcglm: Multivariate Covariance Generalized Linear Models

  For support, collaboration or bug report, visit: 
    http://mcglm.leg.ufpr.br/

  mcglm version 0.7.0 (build on 2021-07-07) is now loaded.
----------------------------------------------------------------------
Loading required package: Matrix
Loading required package: mvtnorm
Loading required package: tweedie
Quitting from lines 52-80 (UniModels.Rmd) 
Error: processing vignette 'UniModels.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building 'UniModels.Rmd'

SUMMARY: processing the following files failed:
  'GLMExamples.Rmd' 'UniModels.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/mcmcse.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
  'LazyDataCompression' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/metaBMA.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'genuMet'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.8Mb
    doc    3.6Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'microcontax.data'
Package unavailable to check Rd xrefs: 'microcontax.data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    lib    1.0Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'missForest_1.5.Rnw' using Sweave
Loading required package: foreach
Loading required package: missForest
Warning in file(file, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'

Error: processing vignette 'missForest_1.5.Rnw' failed with diagnostics:
 chunk 15 (label = muskData) 
Error in file(file, "r") : cannot open the connection

--- failed re-building 'missForest_1.5.Rnw'

SUMMARY: processing the following file failed:
  'missForest_1.5.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 54.5Mb
  sub-directories of 1Mb or more:
    libs  54.1Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Error(s) in re-building vignettes:
--- re-building 'a_1_getting_started.Rmd' using rmarkdown
--- finished re-building 'a_1_getting_started.Rmd'

--- re-building 'a_2_mlrCPO_core.Rmd' using rmarkdown
Quitting from lines 436-437 (a_2_mlrCPO_core.Rmd) 
Error: processing vignette 'a_2_mlrCPO_core.Rmd' failed with diagnostics:
For learner classif.fnn please install the following packages: FNN
--- failed re-building 'a_2_mlrCPO_core.Rmd'

--- re-building 'a_3_all_CPOs.Rmd' using rmarkdown
--- finished re-building 'a_3_all_CPOs.Rmd'

--- re-building 'a_4_custom_CPOs.Rmd' using rmarkdown
--- finished re-building 'a_4_custom_CPOs.Rmd'

--- re-building 'z_1_getting_started_terse.Rmd' using rmarkdown
--- finished re-building 'z_1_getting_started_terse.Rmd'

--- re-building 'z_2_mlrCPO_core_terse.Rmd' using rmarkdown
--- finished re-building 'z_2_mlrCPO_core_terse.Rmd'

--- re-building 'z_3_all_CPOs_terse.Rmd' using rmarkdown
--- finished re-building 'z_3_all_CPOs_terse.Rmd'

--- re-building 'z_4_custom_CPOs_terse.Rmd' using rmarkdown
--- finished re-building 'z_4_custom_CPOs_terse.Rmd'

SUMMARY: processing the following file failed:
  'a_2_mlrCPO_core.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.5Mb
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    libs  21.1Mb
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'alstructure'

Package which this enhances but not available for checking: 'MoBPSmaps'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    extdata   1.6Mb
    libs      2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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    R      1.2Mb
    doc    1.7Mb
    libs   2.5Mb
installed size is  7.3Mb
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    data   2.1Mb
installed size is 14.7Mb
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    htmlwidgets  14.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
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    data   2.0Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    libs     2.3Mb
    raster   2.2Mb
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(motifr)
  > library(reticulate)
  > 
  > test_check("motifr")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]
  
  == Failed tests ================================================================
  -- Error (test-core.R:43:3): io_undirected_dummy_net_issue#27 ------------------
  <Rcpp::exception/C++Error/error/condition>
  Error in `py_call_impl(callable, dots$args, dots$keywords)`: TypeError: 'float' object cannot be interpreted as an integer
  
  Backtrace:
       x
    1. +-reticulate::py_suppress_warnings(motif_summary(ml_net27, lvl_attr = "lvl")) at test-core.R:43:2
    2. | +-base::with(warnings$catch_warnings(), expr)
    3. | \-reticulate:::with.python.builtin.object(...)
    4. |   +-base::tryCatch(...)
    5. |   | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
    6. |   \-base::force(expr)
    7. \-motifr::motif_summary(ml_net27, lvl_attr = "lvl")
    8.   \-motifr::motifs_distribution(...)
    9.     \-pkg.env$sma$distributionMotifsAutoR(...)
   10.       \-reticulate:::py_call_impl(callable, dots$args, dots$keywords)
  -- Error (test-count_motifs.R:101:3): exemplify_motif --------------------------
  <Rcpp::exception/C++Error/error/condition>
  Error in `py_call_impl(callable, dots$args, dots$keywords)`: StopIteration
  
  Backtrace:
      x
   1. +-testthat::expect_null(...) at test-count_motifs.R:101:2
   2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
   3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
   4. \-motifr::exemplify_motif(motifr::tidygraph_dummy_net, "1,2[I.B]")
   5.   \-pkg.env$sma$exemplifyMotif(py_g, motif)
   6.     \-reticulate:::py_call_impl(callable, dots$args, dots$keywords)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]
  Error: Test failures
  Execution halted
installed size is  5.3Mb
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    data   2.0Mb
    libs   2.5Mb
installed size is  5.7Mb
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    R      1.4Mb
    libs   1.9Mb
Package suggested but not available for checking: 'corpus.useR.2008.abstracts'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/mpmi.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   4.1Mb
    libs   2.4Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'leukemiasEset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  12.7Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    1.1Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     4.8Mb
    models   1.1Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Error(s) in re-building vignettes:
--- re-building 'neighbours.Rnw' using Sweave
Loading required namespace: NMOF
Loading required namespace: quadprog
Warning in par(old.par) : graphical parameter "cin" cannot be set
Warning in par(old.par) : graphical parameter "cra" cannot be set
Warning in par(old.par) : graphical parameter "csi" cannot be set
Warning in par(old.par) : graphical parameter "cxy" cannot be set
Warning in par(old.par) : graphical parameter "din" cannot be set
Warning in par(old.par) : graphical parameter "page" cannot be set
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "neighbours.tex" --max-iterations=20 -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'neighbours.Rnw' failed with diagnostics:
running 'texi2dvi' on 'neighbours.tex' failed

LaTeX errors:
! LaTeX Error: File `libertinus.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)


--- failed re-building 'neighbours.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.1/NestedCategBayesImpute.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.3Mb
Package suggested but not available for checking: 'fastshp'
'LazyData' is specified without a 'data' directory
Packages required and available but unsuitable versions: 'stats', 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    CppCode   2.8Mb
    R         6.2Mb
    include   5.8Mb
    libs      2.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/nleqslv.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    doc       5.7Mb
    extdata   1.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
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    doc    2.0Mb
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    libs   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'library' or 'require' call not declared from: 'name'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Package suggested but not available for checking: 'cmdstanr'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'unix'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    exampledata   1.5Mb
    libs          2.7Mb
GNU make is a SystemRequirements.
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs   24.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    R        2.6Mb
    libs     8.2Mb
    models   4.7Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Package suggested but not available for checking: 'openNLPmodels.en'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.7Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.8Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/OptiSembleForecasting.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rrelaxiv'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    libs   2.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'basic-usage.Rmd' using rmarkdown
trying URL 'https://c14.arch.ox.ac.uk/OxCalDistribution.zip'
Content type 'application/zip' length 4396004 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
MCMC analysis
Sort	Burn	Trial	Save	Shrink	kPasses	Done	Ok	Convergence
[.]	[.]	[.]	[.]		3.0	10.0	100.0	100.0
[.]	[.]	[.]	[.]		6.0	20.0	100.0	60.5
[.]	[.]	[.]	[.]		12.0	22.2	100.0	82.7
[.]	[.]	[.]	[.]	[.]	24.0	22.2	100.0	91.3
[.]	[.]	[.]	[.]		48.0	22.2	100.0	93.7
[.]	[.]	[.]	[.]		96.0	22.2	100.0	97.6
[.]	[.]	[.]	[.]		144.0	33.3	100.0	97.6
[.]	[.]	[.]	[.]		192.0	44.4	100.0	97.6
[.]	[.]	[.]	[.]		240.0	55.6	100.0	97.6
[.]	[.]	[.]	[.]		288.0	66.7	100.0	97.6
[.]	[.]	[.]	[.]		336.0	77.8	100.0	97.6
[.]	[.]	[.]	[.]		384.0	88.9	100.0	97.6
[.]	[.]	[.]	[.]		432.0	100.0	100.0	97.6
[.]	[.]	[.]	[.]		480.0	111.1	100.0	97.6
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'basic-usage.Rmd'

SUMMARY: processing the following file failed:
  'basic-usage.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    doc    1.3Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    library  30.0Mb
Package which this enhances but not available for checking: 'CorShrink'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'overview.Rmd' using rmarkdown

Attaching package: 'paleobuddy'

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

    co2

Error: processing vignette 'overview.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Checking should be performed on sources prepared by 'R CMD build'.
GNU make is a SystemRequirements.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.5Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.9Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/pcFactorStan.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs   13.6Mb
    share  12.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'PeakSegJoint-Ex.R' failed
The error most likely occurred in:

> ### Name: PeakSegJointError
> ### Title: PeakSegJointError
> ### Aliases: PeakSegJointError
> 
> ### ** Examples
> 
> 
> library(PeakSegJoint)
> data(H3K36me3.TDH.other.chunk1, envir=environment())
> lims <- c(43000000, 43200000) # left
> some.counts <-
+   subset(H3K36me3.TDH.other.chunk1$counts,
+          lims[1] < chromEnd & chromStart < lims[2])
> some.regions <-
+   subset(H3K36me3.TDH.other.chunk1$regions,
+          lims[1] < chromEnd & chromStart < lims[2])
> fit <- PeakSegJointSeveral(some.counts)
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > suite <- Sys.getenv("TEST_SUITE")
  > if(suite=="")suite <- NULL
  > test_check("PeakSegJoint", filter=suite)
  Loading required package: PeakSegJoint
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   4.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/pema.Rcheck/00install.out' for details.
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11131 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11131 (sockconn)
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs        2.0Mb
    xvg-files   3.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dendextendRcpp'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Note: possible error in 'simplify2array(msg, except = 0L)': unused argument (except = 0) 
See 'd:/Rcompile/CRANpkg/local/4.1/personalized.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'.
xgb_cv_personalized: possible error in simplify2array(msg, except =
  0L): unused argument (except = 0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    application   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
    libs      2.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
at_trans : <anonymous>: no visible global function definition for
  'viewportTransform'
at_trans : <anonymous>: no visible global function definition for
  'groupShear'
at_trans : <anonymous>: no visible global function definition for
  'groupFlip'
grobCoords.pp_grobCoords: no visible global function definition for
  'emptyGrobCoords'
grobCoords.pp_ps_transformation: no visible global function definition
  for 'emptyGrobCoords'
makeContent.pp_transformation: no visible global function definition
  for 'defineGrob'
makeContent.pp_transformation: no visible global function definition
  for 'useGrob'
transformationGrob: no visible binding for global variable
  'viewportTransform'
xylists_to_grobcoords: no visible global function definition for
  'emptyGrobCoords'
xylists_to_grobcoords: no visible global function definition for
  'gridCoords'
xylists_to_grobcoords : <anonymous>: no visible global function
  definition for 'gridCoords'
xylists_to_grobcoords: no visible global function definition for
  'gridGrobCoords'
Undefined global functions or variables:
  defineGrob emptyGrobCoords gridCoords gridGrobCoords groupFlip
  groupShear useGrob viewportTransform
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ggsubplot'
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    bin    8.6Mb
    doc    1.2Mb
    libs   1.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'monocle3', 'ProjecTILs', 'SeuratWrappers'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    tests   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pollimetrydata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   2.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.1Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(popsom)
  > 
  > test_check("popsom")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  
  == Failed tests ================================================================
  -- Failure (test-predict.R:12:3): map.predict function works -------------------
  p[56, 1] (`actual`) not equal to "versicolor" (`expected`).
  
  `actual`:   "virginica" 
  `expected`: "versicolor"
  -- Failure (test-predict.R:13:3): map.predict function works -------------------
  p[145, 1] (`actual`) not equal to "virginica" (`expected`).
  
  `actual`:   "versicolor"
  `expected`: "virginica" 
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  Error: Test failures
  Execution halted
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(popsom)
  > 
  > test_check("popsom")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  
  == Failed tests ================================================================
  -- Failure (test-predict.R:12:3): map.predict function works -------------------
  p[56, 1] (`actual`) not equal to "versicolor" (`expected`).
  
  `actual`:   "virginica" 
  `expected`: "versicolor"
  -- Failure (test-predict.R:13:3): map.predict function works -------------------
  p[145, 1] (`actual`) not equal to "virginica" (`expected`).
  
  `actual`:   "versicolor"
  `expected`: "virginica" 
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Loading_and_manipulating.Rmd' using rmarkdown
Error: processing vignette 'Loading_and_manipulating.Rmd' failed with diagnostics:
Using anchor_sections requires Pandoc 2.0+
--- failed re-building 'Loading_and_manipulating.Rmd'

--- re-building 'full_pattern_summation.Rmd' using rmarkdown
Error: processing vignette 'full_pattern_summation.Rmd' failed with diagnostics:
Using anchor_sections requires Pandoc 2.0+
--- failed re-building 'full_pattern_summation.Rmd'

SUMMARY: processing the following files failed:
  'Loading_and_manipulating.Rmd' 'full_pattern_summation.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinyApp   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gurobi', 'Rcplex'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.8Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    4.6Mb
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      2.3Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/ProjectionBasedClustering.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/prophet.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.4Mb
installed size is  5.0Mb
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    libs   4.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.3Mb
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rdt'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'MI_boot.Rmd' using rmarkdown
--- finished re-building 'MI_boot.Rmd'

--- re-building 'MI_cv_naive.Rmd' using rmarkdown
--- finished re-building 'MI_cv_naive.Rmd'

--- re-building 'Pool_Model_Performance.Rmd' using rmarkdown
--- finished re-building 'Pool_Model_Performance.Rmd'

--- re-building 'Pooling_AUC_values.Rmd' using rmarkdown
--- finished re-building 'Pooling_AUC_values.Rmd'

--- re-building 'boot_MI.Rmd' using rmarkdown
--- finished re-building 'boot_MI.Rmd'

--- re-building 'cv_MI.Rmd' using rmarkdown
--- finished re-building 'cv_MI.Rmd'

--- re-building 'cv_MI_RR.Rmd' using rmarkdown
--- finished re-building 'cv_MI_RR.Rmd'

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

Attaching package: 'mice'

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

    filter

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

    cbind, rbind

--- finished re-building 'development_workflow.Rmd'

--- re-building 'psfmi_CoxModels.Rmd' using rmarkdown
--- finished re-building 'psfmi_CoxModels.Rmd'

--- re-building 'psfmi_LinearModels.Rmd' using rmarkdown
--- finished re-building 'psfmi_LinearModels.Rmd'

--- re-building 'psfmi_LogisticModels.Rmd' using rmarkdown
--- finished re-building 'psfmi_LogisticModels.Rmd'

--- re-building 'psfmi_StabilityAnalysis.Rmd' using rmarkdown
Quitting from lines 60-78 (psfmi_StabilityAnalysis.Rmd) 
Error: processing vignette 'psfmi_StabilityAnalysis.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'psfmi_StabilityAnalysis.Rmd'

--- re-building 'psfmi_mice.Rmd' using rmarkdown
--- finished re-building 'psfmi_mice.Rmd'

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

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

> ### Name: impactsnopar
> ### Title: Compute direct, indirect and total impacts functions for
> ###   continous non-parametric covariates in semiparametric spatial
> ###   regression models.
> ### Aliases: impactsnopar
> 
> ### ** Examples
> 
> ################################################
> # Examples using spatial data of Ames Houses.
> ###############################################
> # Getting and preparing the data
> library(pspatreg)
> library(spdep)
Loading required package: sp
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')`
Loading required package: sf
Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 7.2.1; sf_use_s2() is TRUE
> library(sf)
> ames <- AmesHousing::make_ames() # Raw Ames Housing Data
> ames_sf <- st_as_sf(ames, coords = c("Longitude", "Latitude"))
> ames_sf$Longitude <- ames$Longitude
> ames_sf$Latitude <- ames$Latitude
> ames_sf$lnSale_Price <- log(ames_sf$Sale_Price)
> ames_sf$lnLot_Area <- log(ames_sf$Lot_Area)
> ames_sf$lnTotal_Bsmt_SF <- log(ames_sf$Total_Bsmt_SF+1)
> ames_sf$lnGr_Liv_Area <- log(ames_sf$Gr_Liv_Area)
> ########### Constructing the spatial weights matrix
> ames_sf1 <- ames_sf[(duplicated(ames_sf$Longitude) == FALSE), ]
> coord_sf1 <- cbind(ames_sf1$Longitude, ames_sf1$Latitude)
> ID <- row.names(as(ames_sf1, "sf"))
> col_tri_nb <- tri2nb(coord_sf1)
> soi_nb <- graph2nb(soi.graph(col_tri_nb, 
+                             coord_sf1), 
+                    row.names = ID)
Error in soi.graph(col_tri_nb, coord_sf1) : dbscan required
Calls: graph2nb -> soi.graph
Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    libs         1.3Mb
    staticdocs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
NB: this package is only installed for sub-architecture 'x64'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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    doc    4.4Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      5.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      2.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   2.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.9Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'queryup-Ex.R' failed
The error most likely occurred in:

> ### Name: get_uniprot_data
> ### Title: Retrieve data from UniProt using UniProt's REST API
> ### Aliases: get_uniprot_data
> 
> ### ** Examples
> 
> #Getting gene names, keywords and protein sequences for a set of UniProt IDs.
> ids <- c("P22682", "P47941")
> cols <- c("accession", "id", "gene_names", "keyword", "sequence")
> query = list("accession_id" = ids)
> df <- get_uniprot_data(query = query, columns = cols)$content
Error in function (type, msg, asError = TRUE)  : 
  error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
Calls: get_uniprot_data ... <Anonymous> -> <Anonymous> -> curlPerform -> <Anonymous> -> fun
Execution halted
Error(s) in re-building vignettes:
--- re-building 'queryup.Rmd' using rmarkdown
Quitting from lines 31-34 (queryup.Rmd) 
Error: processing vignette 'queryup.Rmd' failed with diagnostics:
error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
--- failed re-building 'queryup.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! pdfTeX error (ext4): \pdfendlink ended up in different nesting level than \pd
fstartlink.
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1 \begin{theindex}
!  ==> Fatal error occurred, no output PDF file produced!
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
'library' or 'require' call to 'RDCOMClient' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc           5.2Mb
    htmlwidgets   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.6Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   6.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      3.8Mb
    libs   2.0Mb
Running examples in 'rangeBuilder-Ex.R' failed
The error most likely occurred in:

> ### Name: coordError
> ### Title: Coordinate error
> ### Aliases: coordError
> 
> ### ** Examples
> 
> data(crotalus)
> 
> xy <- crotalus[1:100, c('decimallongitude','decimallatitude')]
> 
> coordError(xy)

  |                                                  | 0 % ~calculating  Error in sp::spTransform(pts, CRS("+proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +ellps=WGS84 +units=m +no_defs")) : 
  package rgdal is required for spTransform methods
Calls: coordError -> <Anonymous> -> FUN -> <Anonymous> -> <Anonymous>
Execution halted
Running examples in 'rangeBuilder-Ex.R' failed
The error most likely occurred in:

> ### Name: coordError
> ### Title: Coordinate error
> ### Aliases: coordError
> 
> ### ** Examples
> 
> data(crotalus)
> 
> xy <- crotalus[1:100, c('decimallongitude','decimallatitude')]
> 
> coordError(xy)

  |                                                  | 0 % ~calculating  Error in sp::spTransform(pts, CRS("+proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +ellps=WGS84 +units=m +no_defs")) : 
  package rgdal is required for spTransform methods
Calls: coordError -> <Anonymous> -> FUN -> <Anonymous> -> <Anonymous>
Execution halted
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.5Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/rater.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   1.0Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.1/Rblpapi.Rcheck/00install.out' for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/rcbayes.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    cont  25.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/RcmdrPlugin.survival.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'ROpenOffice'
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.2Mb
    po    2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      2.3Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    include  44.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    lib       4.6Mb
GNU make is a SystemRequirements.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      2.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    include        1.5Mb
    jsonexamples   3.8Mb
    libs           3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/rcrypt.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'R.devices-overview.tex.rsp' using rsp
R.devices v2.17.1 (2022-06-21 08:00:02 UTC) successfully loaded. See ?R.devices for help.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "R.devices-overview.tex" --max-iterations=20 -I "d:/RCompile/CRANpkg/local/4.1/R.devices.Rcheck/vign_test/R.devices/vignettes" -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'R.devices-overview.tex.rsp' failed with diagnostics:
running 'texi2dvi' on 'R.devices-overview.tex' failed

LaTeX errors:
devices-overview.tex:55: LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help
You're in trouble here.  Try typing  <return>  to proceed.

--- failed re-building 'R.devices-overview.tex.rsp'

SUMMARY: processing the following file failed:
  'R.devices-overview.tex.rsp'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    data   1.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dataui'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/recometrics.Rcheck/00install.out' for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'ExampleBinary.md' using md
Error: processing vignette 'ExampleBinary.md' failed with diagnostics:
there is no package called 'markdown'
--- failed re-building 'ExampleBinary.md'

--- re-building 'ExampleGauss.md' using md
Error: processing vignette 'ExampleGauss.md' failed with diagnostics:
there is no package called 'markdown'
--- failed re-building 'ExampleGauss.md'

--- re-building 'introremiod.md' using md
Error: processing vignette 'introremiod.md' failed with diagnostics:
there is no package called 'markdown'
--- failed re-building 'introremiod.md'

SUMMARY: processing the following files failed:
  'ExampleBinary.md' 'ExampleGauss.md' 'introremiod.md'

Error: Vignette re-building failed.
Execution halted
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'repoRter_nih.Rmd' using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

This is your JSON payload:
{
    "criteria": {
        "covid_response": [
            "All"
        ],
        "use_relevance": false,
        "include_active_projects": false,
        "exclude_subprojects": false,
        "multi_pi_only": false,
        "newly_added_projects_only": false,
        "sub_project_only": false
    },
    "include_fields": [
        "AwardAmount",
        "CovidResponse"
    ],
    "offset": 0,
    "limit": 500
}

If you receive a non-200 API response, compare this formatting (boxes, braces, quotes, etc.) to the 'Complete Payload' schema provided here:
https://api.reporter.nih.gov/?urls.primaryName=V2.0#/Search/post_v2_projects_search 

Retrieving first page of results (up to 500 records)
Retrieving results 501 to 1000 of 3222
Retrieving results 1001 to 1500 of 3222
Retrieving results 1501 to 2000 of 3222
Retrieving results 2001 to 2500 of 3222
Retrieving results 2501 to 3000 of 3222
Retrieving results 3001 to 3222 of 3222
! Undefined control sequence.
l.68 \UseRawInputEncoding

Error: processing vignette 'repoRter_nih.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/repoRter.nih.Rcheck/vign_test/repoRter.nih/vignettes/repoRter_nih.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See repoRter_nih.log for more info.
--- failed re-building 'repoRter_nih.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs      2.5Mb
    swagger   1.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs      3.3Mb
    models    1.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    doc       3.8Mb
    extdata   2.6Mb
    java     26.1Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/Rforestry.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 112.7Mb
  sub-directories of 1Mb or more:
    doc        3.7Mb
    gdal       2.2Mb
    libs      94.3Mb
    pictures   1.3Mb
    proj       8.7Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      2.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc     1.1Mb
    fonts   1.5Mb
    libs    2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    lib    6.6Mb
    libs   8.2Mb
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
    libs     15.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.2Mb
Found the following possibly unsafe calls:
File 'rJava/R/import.R':
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File 'rJava/R/jinit.R':
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.1/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/4.1/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    extdata  23.9Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs    4.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    rmd   8.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/rmBayes.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs       2.1Mb
    minizinc   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
GNU make is a SystemRequirements.
Found the following significant warnings:
  RlibMVL.c:1446:9: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.1/RMVL.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
Missing or unexported object: 'SummarizedExperiment::colnames'
Package suggested but not available for checking: 'rnaturalearthhires'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doxygen   1.4Mb
    libs      3.0Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              4.2Mb
    simulationStudy   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
evalMedian: no visible global function definition for 'xtabs'
evalMode: no visible global function definition for 'xtabs'
rpartScore: no visible global function definition for 'model.extract'
rpartScore: no visible global function definition for 'var'
rpartScore: no visible binding for global variable 'var'
splitAbs: no visible global function definition for 'xtabs'
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
GNU make is a SystemRequirements.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.1/Rserve/libs/i386/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/4.1/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'STARSmanual.ltx' using tex
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "STARSmanual.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'STARSmanual.ltx' failed with diagnostics:
running 'texi2dvi' on 'STARSmanual.ltx' failed

BibTeX errors:
I couldn't open database file bibliography.bib.bib
---line 12 of file STARSmanual.aux
 : \bibdata{bibliography.bib
 :                          }
I'm skipping whatever remains of this command
I found no database files---while reading file STARSmanual.aux

--- failed re-building 'STARSmanual.ltx'

SUMMARY: processing the following file failed:
  'STARSmanual.ltx'

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Name: SolrList-class
> ### Title: SolrList
> ### Aliases: class:SolrList SolrList-class length,SolrList-method
> ###   names,SolrList-method [<-,SolrList,ANY,ANY,ANY-method
> ###   [[,SolrList,ANY-method [,SolrList-method [[,SolrList-method
> ###   [[<-,SolrList-method unique,SolrList-method searchDocs
> ###   searchDocs,Solr SolrList coerce,Solr,SolrList-method
> ###   coerce,SolrList,DocCollection-method show,SolrList-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  4.93 0.12 5.07 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Running examples in 'rsparse-Ex.R' failed
The error most likely occurred in:

> ### Name: WRMF
> ### Title: Weighted Regularized Matrix Factorization for collaborative
> ###   filtering
> ### Aliases: WRMF
> 
> ### ** Examples
> 
> data('movielens100k')
> train = movielens100k[1:900, ]
> cv = movielens100k[901:nrow(movielens100k), ]
> model = WRMF$new(rank = 5,  lambda = 0, feedback = 'implicit')
> user_emb = model$fit_transform(train, n_iter = 5, convergence_tol = -1)
Error in library.dynam(lib, package, package.lib) : 
  DLL 'MatrixExtra' not found: maybe not installed for this architecture?
Calls: <Anonymous> -> loadNamespace -> library.dynam
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(rsparse)
  Loading required package: Matrix
  > library(data.table)
  > library(Matrix)
  > options(rsparse_omp_threads = 1L)
  > logger = lgr::get_logger('rsparse')
  > logger$set_threshold('warn')
  > data("movielens100k")
  > test_check("rsparse")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 44 ]
  
  == Failed tests ================================================================
  -- Error (test-wrmf.R:49:5): test WRMF core ------------------------------------
  Error in `library.dynam(lib, package, package.lib)`: DLL 'MatrixExtra' not found: maybe not installed for this architecture?
  Backtrace:
      x
   1. +-model$fit_transform(train, n_iter = 5, convergence_tol = -1) at test-wrmf.R:49:4
   2. \-base::loadNamespace(x)
   3.   \-base::library.dynam(lib, package, package.lib)
  -- Error (test-wrmf.R:86:5): test WRMF FLOAT -----------------------------------
  Error in `library.dynam(lib, package, package.lib)`: DLL 'MatrixExtra' not found: maybe not installed for this architecture?
  Backtrace:
      x
   1. +-model$fit_transform(train, n_iter = 5, convergence_tol = -1) at test-wrmf.R:86:4
   2. \-base::loadNamespace(x)
   3.   \-base::library.dynam(lib, package, package.lib)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 44 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.2Mb
    help   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.8Mb
    libs  17.4Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    lib    3.8Mb
    libs   9.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    libs  29.7Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    rmarkdown   6.6Mb
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.3Mb
    projects   2.7Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data      3.4Mb
    extdata   1.4Mb
    libs      2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   5.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/rts2.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'glmmADMB'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs      8.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   9.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Package suggested but not available for checking: 'unix'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    exdata   2.4Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   6.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
parse.SAScii: no visible binding for global variable 'end'
parse.SAScii: no visible binding for global variable 'start'
read.SAScii: no visible global function definition for 'download.file'
read.SAScii: no visible global function definition for 'unzip'
read.SAScii: no visible global function definition for 'read.fwf'
read.SAScii: no visible global function definition for 'capture.output'
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.2Mb
GNU make is a SystemRequirements.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R         1.6Mb
    extdata   1.3Mb
    libs      2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   2.5Mb
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using rmarkdown
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'prettydoc'
--- failed re-building 'tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   3.8Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs     6.7Mb
    models   1.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 113.2Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    gdal     2.2Mb
    libs    96.1Mb
    proj     8.7Mb
    sqlite   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'sglasso-Ex.R' failed
The error most likely occurred in:

> ### Name: klcv
> ### Title: Cross-Validated Kullback-Leibler Divergence
> ### Aliases: klcv print.klcv
> ### Keywords: models
> 
> ### ** Examples
> 
> N <- 100
> p <- 5
> X <- matrix(rnorm(N * p), N, p)
> S <- crossprod(X) / N
> mask <- outer(1:p, 1:p, function(i,j) 0.5^abs(i-j))
> mask[1,5] <- mask[1,4] <- mask[2,5] <- NA
> mask[5,1] <- mask[4,1] <- mask[5,2] <- NA
> out.sglasso_path <- sglasso(S, mask, tol = 1.0e-13)
Warning in sglasso.fit(Sv = S@x, mask = mask, w = w, flg = flg, nrho = nrho,  :
  sglasso does not converge with code 2

> out.klcv <- klcv(out.sglasso_path, X)
Error in klcv(out.sglasso_path, X) : error in dpotrf or dpotri subroutine
Execution halted
Running examples in 'sglasso-Ex.R' failed
The error most likely occurred in:

> ### Name: klcv
> ### Title: Cross-Validated Kullback-Leibler Divergence
> ### Aliases: klcv print.klcv
> ### Keywords: models
> 
> ### ** Examples
> 
> N <- 100
> p <- 5
> X <- matrix(rnorm(N * p), N, p)
> S <- crossprod(X) / N
> mask <- outer(1:p, 1:p, function(i,j) 0.5^abs(i-j))
> mask[1,5] <- mask[1,4] <- mask[2,5] <- NA
> mask[5,1] <- mask[4,1] <- mask[5,2] <- NA
> out.sglasso_path <- sglasso(S, mask, tol = 1.0e-13)
Warning in sglasso.fit(Sv = S@x, mask = mask, w = w, flg = flg, nrho = nrho,  :
  sglasso does not converge with code 2

> out.klcv <- klcv(out.sglasso_path, X)
Error in klcv(out.sglasso_path, X) : error in dpotrf or dpotri subroutine
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hydromad'
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    www   6.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/SIGN.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/simer.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.7Mb
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rPython'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.4Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/snplist.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     3.2Mb
    doc   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    2.1Mb
    libs   3.4Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/4.1/SongEvo.Rcheck/
vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20population\%2
0size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/SongEvo.Rcheck/vign_test/SongEvo/vignettes/SongEvo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SongEvo.log for more info.
--- failed re-building 'SongEvo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.0Mb
Package suggested but not available for checking: 'r2cytoscape'
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      5.1Mb
'LazyData' is specified without a 'data' directory
Running 'test-all.R' [104s]
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: 'SpaDES.core'
  
  The following objects are masked from 'package:stats':
  
      end, start
  
  The following object is masked from 'package:utils':
  
      citation
  
  trying URL 'https://www.zotero.org/styles/ecology-letters'
    adding: test.qs (stored 0%)
    adding: TransferFolder/cache.db (stored 0%)
    adding: TransferFolder/yCRp86x.grd (deflated 31%)
    adding: TransferFolder/yCRp86x.gri (deflated 55%)
    adding: TransferFolder/yCRp86x_1.grd (deflated 31%)
    adding: TransferFolder/yCRp86x_1.gri (deflated 55%)
    adding: TransferFolder/yCRp86x_2.grd (deflated 31%)
    adding: TransferFolder/yCRp86x_2.gri (deflated 55%)
    adding: temp/Rtmp23hujH/JHJXYi/landscape_month1.rds (stored 0%)
  [ FAIL 1 | WARN 0 | SKIP 21 | PASS 651 ]
  
  == Skipped tests ===============================================================
  * On CRAN (12)
  * On Windows (1)
  * benchmarking DES (1)
  * empty test (4)
  * interactive() is not TRUE (1)
  * restartR not possible in automated tests (1)
  * restartR with logging not possible in automated tests (1)
  
  == Failed tests ================================================================
  -- Error (<text>:6:3): module templates work -----------------------------------
  Error in `download.file("https://www.zotero.org/styles/ecology-letters", 
      destfile = "citations/ecology-letters.csl")`: cannot open URL 'https://www.zotero.org/styles/ecology-letters'
  Backtrace:
      x
   1. \-utils::download.file(...)
  
  [ FAIL 1 | WARN 0 | SKIP 21 | PASS 651 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   3.1Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    java   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'spatialEco-Ex.R' failed
The error most likely occurred in:

> ### Name: cgls_urls
> ### Title: Provide URL's for Copernicus Global Land Service datasets
> ### Aliases: cgls_urls
> 
> ### ** Examples
> 
> # Create date string for query
> d <- seq(as.Date("2020/05/01"), as.Date("2020-09-01"), by="day")
> 
> # Search for 300m (333m) LAI within specified date range 
> all.urls <- cgls_urls(dates = d, resolution = 300, 
+                         product = "lai")		
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: cgls_urls -> paste -> readLines -> file
Execution halted
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   2.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    help   2.8Mb
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet', 'spatstat.data', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
    etc   1.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs      3.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.3Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'SRTsim.Rmd' using rmarkdown
Quitting from lines 26-47 (SRTsim.Rmd) 
Error: processing vignette 'SRTsim.Rmd' failed with diagnostics:
there is no package called 'BiocFileCache'
--- failed re-building 'SRTsim.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  21.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   5.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/ssMousetrack.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  arg.c:165:17: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.1/stanette.Rcheck/00install.out' for details.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    lib    3.9Mb
    libs   9.9Mb
GNU make is a SystemRequirements.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    include  10.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'starsdata'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   1.7Mb
    nc    1.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.7Mb
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      2.5Mb
Package suggested but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
Data codoc mismatches from documentation object 'SLCS':
Variables in data frame 'SLCS'
  Code: SLCS_1 SLCS_10 SLCS_11 SLCS_12 SLCS_13 SLCS_14 SLCS_15 SLCS_16
        SLCS_2 SLCS_3 SLCS_4 SLCS_5 SLCS_6 SLCS_7 SLCS_8 SLCS_9 age sex
        user_id
  Docs: SLCS_11 SLCS_1 SLCS_10 SLCS_12 SLCS_13 SLCS_14 SLCS_15 SLCS_16
        SLCS_2 SLCS_3 SLCS_4 SLCS_5 SLCS_6 SLCS_7 SLCS_8 SLCS_9 age sex
        user_id
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.7Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    bin   6.9Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.2Mb
Malformed Title field: should not end in a period.
Package required and available but unsuitable version: 'stringi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/string2path.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/stringi.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'STRaitRazoR'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   2.4Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc  12.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.3Mb
    libs   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/surveil.Rcheck/00install.out' for details.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.4Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'swephRdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cplexAPI'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
Package suggested but not available for checking: 'cplexAPI'
Package suggested but not available for checking: 'cplexAPI'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs     6.3Mb
    mylibs   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'unix'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tashudata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    apps   1.4Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/telefit.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       3.7Mb
    libs      2.2Mb
    telemac   1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/terra.Rcheck/00install.out' for details.
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs      14.5Mb
    tessdata  14.0Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.0Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   2.9Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
Error(s) in re-building vignettes:
--- re-building 'theft.Rmd' using rmarkdown
No IDs removed. All value vectors good for feature extraction.
Running computations for catch22...
Warning: As of 0.1.14 the feature 'CO_f1ecac' returns a double instead of int
This warning is displayed once per session.

Calculations completed for catch22.
Null testing method 'model free shuffles' is fast. Consider running more permutations for more reliable results. N = 10000 is recommended.
Quitting from lines 283-301 (theft.Rmd) 
Error: processing vignette 'theft.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'theft.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    data   3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
GNU make is a SystemRequirements.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    test_db   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   4.4Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   1.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   5.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'TKCat-User-guide.Rmd' using rmarkdown
Loading required package: ReDaMoR
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: magrittr
Loading required package: visNetwork

Attaching package: 'ReDaMoR'

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

    lengths

Loading required package: DBI
Rows: 500 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (3): id, name, description
dbl (1): level

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 1903 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): db, label
dbl (1): id

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2594 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): db, hp
dbl (1): id

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Quitting from lines 193-197 (TKCat-User-guide.Rmd) 
Error: processing vignette 'TKCat-User-guide.Rmd' failed with diagnostics:
This function need 'igraph' package to compute layout. Please 
         install it before.
--- failed re-building 'TKCat-User-guide.Rmd'

SUMMARY: processing the following file failed:
  'TKCat-User-guide.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    examples  19.6Mb
    include    3.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'corpus.JSS.papers'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    R         4.8Mb
    help      1.6Mb
    include   1.3Mb
    libs     28.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'toscaData'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taxidata'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  20.4Mb
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'TreeDistData'
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    libs       2.2Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/trialr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'sl3'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     7.0Mb
    ubinc   2.0Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   7.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    help   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  23.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'USAboundariesData'
Package suggested but not available for checking: 'USA.state.boundaries.data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(usincometaxes)
  > 
  > test_check("usincometaxes")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 9 ]
  
  == Failed tests ================================================================
  -- Error (test-calculate_taxes.R:98:3): All interface options return same values --
  Error: There was a problem in calculating the taxes using 'ssh'.
  Please try a different `interface` option.
  Alternatively, you can try manually uploading the data to TAXSIM as an avenue of troubleshooting.
  See the following address for more information: https://www.shaneorr.io/r/usincometaxes/articles/send-data-to-taxsim.html
  Backtrace:
      x
   1. \-usincometaxes::taxsim_calculate_taxes(...) at test-calculate_taxes.R:98:2
   2.   \-base::tryCatch(...)
   3.     \-base (local) tryCatchList(expr, classes, parentenv, handlers)
   4.       \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5.         \-value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 9 ]
  Error: Test failures
  Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   6.6Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  23.2Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   5.0Mb
Running 'testthat.R' [20s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(VAJointSurv)
  Loading required package: survival
  > 
  > options(testthat.progress.max_fails = 1000)
  > test_check("VAJointSurv")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 6094 ]
  
  == Skipped tests ===============================================================
  * On CRAN (3)
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 6094 ]
  > 
  > proc.time()
     user  system elapsed 
    19.34    0.51   19.85 
  Error: bad value
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'VedicDateTime.Rmd' using rmarkdown
Error: processing vignette 'VedicDateTime.Rmd' failed with diagnostics:
Using a custom highlighting style requires Pandoc 2.0 and above
--- failed re-building 'VedicDateTime.Rmd'

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

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

> ### Name: from_spec
> ### Title: Take a JSON Vega-Lite Spec and render as an htmlwidget
> ### Aliases: from_spec
> 
> ### ** Examples
> 
> from_spec("http://rud.is/dl/embedded.json")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung wurde zurückgesetzt.'
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    help   2.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    ext   4.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   8.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc           2.5Mb
    htmlwidgets   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    6.3Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Package suggested but not available for checking: 'prepr'
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/WINS.Rcheck/vign_test/WINS/vignettes/vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See vignette.log for more info.
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
Malformed Title field: should not end in a period.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    java  34.2Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/xml2.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'spelling.R' [0s]
  Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ymlthis)
  > 
  > test_check("ymlthis")
  Loading required namespace: blogdown
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 28 ]
  
  == Skipped tests ===============================================================
  * On CRAN (3)
  
  == Failed tests ================================================================
  -- Error (test-blogdown_yaml.R:5:3): multiplication works ----------------------
  Error: Invalid argument in YAML output function bookdown::gitbook(lib_dir = "assets", split_by = "section", config = gitbook_config(toolbar_position = "static"))
  Error: Using anchor_sections requires Pandoc 2.0+
  
  Backtrace:
       x
    1. +-... %>% stringify_yaml() at test-blogdown_yaml.R:5:2
    2. +-ymlthis:::stringify_yaml(.)
    3. | \-x %>% ymlthis:::capture_yml() %>% paste(collapse = "\n") at d:\RCompile\CRANpkg\local\4.1\ymlthis.Rcheck\tests\testthat\helper-utils.R:3:2
    4. +-base::paste(., collapse = "\n")
    5. +-ymlthis:::capture_yml(.)
    6. | +-utils::capture.output(print(.yml))
    7. | | \-base::withVisible(...elt(i))
    8. | \-base::print(.yml)
    9. \-ymlthis::yml_output(...)
   10.   \-ymlthis:::validate_output_yml(x)
   11.     \-purrr::walk(.function_calls, eval_tidy_yml)
   12.       \-purrr::map(.x, .f, ...)
   13.         \-ymlthis (local) .f(.x[[i]], ...)
   14.           \-ymlthis:::stop_yml_eval(out, x)
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 28 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in 'YRmisc-Ex.R' failed
The error most likely occurred in:

> ### Name: xd.fred
> ### Title: Download data from Federal Reserve Bank of St. Louis
> ### Aliases: xd.fred
> 
> ### ** Examples
> 
>  cpi <- xd.fred("CPIAUCSL") # CPI data
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(file, "rt") : cannot open the connection
Calls: xd.fred -> read.csv -> read.table -> file
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(zipangu)
  > 
  > test_check("zipangu")
  [ FAIL 3 | WARN 16 | SKIP 2 | PASS 142 ]
  
  == Skipped tests ===============================================================
  * On CRAN (2)
  
  == Failed tests ================================================================
  -- Failure (test-jyear.R:10:3): convert jyear works ----------------------------
  convert_jyear("<U+5E73><U+6210><U+5143><U+5E74>") not equal to convert_jyear("H1").
  1/1 mismatches
  [1] NA - 1989 == NA
  -- Failure (test-jyear.R:33:3): convert japanese date format -------------------
  convert_jdate("<U+4EE4><U+548C>2<U+5E74>7<U+6708>6<U+65E5>") not equal to as.Date("2020-07-06").
  'is.NA' value mismatch: 0 in current 1 in target
  -- Failure (test-jyear.R:45:3): convert japanese date format -------------------
  convert_jdate(...) not equal to as.Date(c("2018-01-01", "2018-02-01", NA)).
  'is.NA' value mismatch: 1 in current 3 in target
  
  [ FAIL 3 | WARN 16 | SKIP 2 | PASS 142 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'zdat'
Running examples in 'zoon-Ex.R' failed
The error most likely occurred in:

> ### Name: ModuleArguments
> ### Title: ModuleArguments
> ### Aliases: ModuleArguments
> 
> ### ** Examples
> 
> ModuleArguments('Background')
Error in ModuleArguments("Background") : 
  URL for module does not exist: https://raw.githubusercontent.com/zoonproject/modules/master/R/Background.R
Execution halted
'LazyData' is specified without a 'data' directory