installed size is  5.5Mb
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'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   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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installed size is 10.9Mb
  sub-directories of 1Mb or more:
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installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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    doc    3.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
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:
    doc   5.1Mb
'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   6.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
installed size is 22.4Mb
  sub-directories of 1Mb or more:
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    libs  18.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    libs      2.4Mb
'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: ‘usethis’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘fmrs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.8Mb
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Namespace in Imports field not imported from: ‘RiskPortfolios’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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installed size is  9.2Mb
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Package suggested but not available for checking: ‘INLA’
installed size is 48.5Mb
  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
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.9Mb
installed size is 48.0Mb
  sub-directories of 1Mb or more:
    libs  47.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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    libs   2.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
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    libs   4.3Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
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html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘HiddenMarkov’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 60.9Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.3Mb
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installed size is 10.0Mb
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    libs   9.3Mb
'LazyData' is specified without a 'data' directory
Note: found 124 marked UTF-8 strings
installed size is 15.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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installed size is  8.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 68.3Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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    libs   3.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
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    help   1.1Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
'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:
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installed size is  7.7Mb
  sub-directories of 1Mb or more:
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    libs   5.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 44.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘microViz’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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installed size is  5.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
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Package suggested but not available for checking: ‘webshot2’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
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installed size is  5.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 38558 marked UTF-8 strings
installed size is  7.7Mb
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Note: found 1 marked UTF-8 string
Note: found 359 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SparkR’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
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installed size is  6.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
installed size is  7.0Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘LTRCtrees’
Package unavailable to check Rd xrefs: ‘LTRCtrees’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘icd’
installed size is  5.1Mb
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Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is 15.3Mb
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Package suggested but not available for checking: ‘mixAK’
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Note: found 10 marked UTF-8 strings
installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
installed size is 31.1Mb
  sub-directories of 1Mb or more:
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    libs  29.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘IFCdata’
installed size is  7.4Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 23.5Mb
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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  7.1Mb
  sub-directories of 1Mb or more:
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installed size is 14.2Mb
  sub-directories of 1Mb or more:
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installed size is 31.3Mb
  sub-directories of 1Mb or more:
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installed size is 21.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
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'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
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.0Mb
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installed size is  7.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
logLik:
  function(object, ...)
logLik.displacement:
  function(model, ...)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  logLik.displacement
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'logLik.displacement':
  ‘logLik.displacement’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
installed size is 11.7Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'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
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   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.
Namespace in Imports field not imported from: ‘splines2’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
'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  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 30.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘readxl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/intrinsicFRP.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘surveyspec’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data           1.4Mb
    libs           1.8Mb
    shiny-server   1.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rhdf5’
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gmodels’ ‘lmtest’ ‘testthat’ ‘tidyverse’ ‘zoo’
  All declared Imports should be used.
Note: found 46 marked UTF-8 strings
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected`: 6
  ── Failure ('test-dday.R:10:3'): dday works ────────────────────────────────────
  dday(df, "2023-08-01", d = 1, x = "x") (`actual`) not identical to 13 (`expected`).
  
    `actual`:  0
  `expected`: 13
  ── Failure ('test-ytd.R:12:3'): ytd works ──────────────────────────────────────
  ytd(df, "2023-08-01", x = "x") (`actual`) not equal to dday(df, "2023-08-01", x = "x") (`expected`).
  
    `actual`: 10
  `expected`:  0
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 45 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Package suggested but not available for checking: ‘Rmpi’
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘glmnet’
  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  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
Note: found 104 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: ‘rmarkdown’
  All declared Imports should be used.
installed size is 62.8Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.3Mb
    libs  57.6Mb
GNU make is a SystemRequirements.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  11.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Note: found 58 marked UTF-8 strings
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          15.8Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘reshape’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Note: found 2261 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1984 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘mcmcplots’ ‘tidyverse’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/JavaGD.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
installed size is 59.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  54.7Mb
GNU make is a SystemRequirements.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    i18n   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.2Mb
Package which this enhances but not available for checking: ‘remMap’
'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: ‘doParallel’
  All declared Imports should be used.
Note: found 176 marked UTF-8 strings
Package required but not available: ‘scran’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  32.7Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    examples      2.8Mb
    htmlwidgets   1.1Mb
    www           2.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Superpower’ ‘pwr’ ‘shinydashboard’
  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: ‘gifski’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Namespaces in Imports field not imported from:
  ‘EQL’ ‘univariateML’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    help   7.0Mb
'LazyData' is specified without a 'data' directory
apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fitdistrplus’ ‘plotly’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’ using Sweave
Error: processing vignette 'Instruction_of_functions_of_R_package_KINSIMU.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Instruction_of_functions_of_R_package_KINSIMU.tex' failed.
LaTeX errors:
! LaTeX Error: Command \gather already defined.
               Or name \end... illegal, see p.192 of the manual.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! Emergency stop.
 ...                                              
                                                  
l.1560 }
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RGeostats’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
'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:
    data   1.6Mb
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘mice’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 13.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.6Mb
'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:
    R      2.1Mb
    doc    1.7Mb
    help   1.1Mb
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘mixAK’
Package unavailable to check Rd xrefs: ‘mixAK’
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   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
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘chinese.misc’ ‘dplyr’ ‘factoextra’ ‘glasso’
  ‘highcharter’ ‘htmlwidgets’ ‘ldatuning’ ‘qgraph’ ‘quanteda’ ‘rvest’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinycssloaders’
  ‘shinydashboard’ ‘shinyjs’ ‘stringr’ ‘textmineR’ ‘textplot’ ‘tidyr’
  ‘topicmodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘beepr’ ‘broom’ ‘chinese.misc’ ‘dplyr’ ‘highcharter’
  ‘htmlwidgets’ ‘ldatuning’ ‘parallel’ ‘plotly’ ‘purrr’ ‘quanteda’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinycssloaders’ ‘shinyjs’
  ‘stringr’ ‘textmineR’ ‘tidyr’ ‘tidytext’ ‘topicmodels’
  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:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
Note: found 75 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
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 53.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  49.2Mb
GNU make is a SystemRequirements.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   5.9Mb
installed size is 46.2Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  43.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘LFDREmpiricalBayes.Rnw’ using Sweave

Error: processing vignette 'LFDREmpiricalBayes.Rnw' failed with diagnostics:
 chunk 4 (label = generating artificial SNPs) 
Error in library(LFDR.MLE) : there is no package called ‘LFDR.MLE’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  10.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 93.7Mb
  sub-directories of 1Mb or more:
    libs  92.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      9.0Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.5Mb
installed size is 62.0Mb
  sub-directories of 1Mb or more:
    libs  61.3Mb
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 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
Namespace in Imports field not imported from: ‘e1071’
  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: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs      20.1Mb
    testdata   1.3Mb
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    libs  55.7Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R              2.0Mb
    doc-software   2.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 33.7Mb
  sub-directories of 1Mb or more:
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    libs  31.7Mb
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lestat’
  All declared Imports should be used.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’
Note: found 12 marked UTF-8 strings
'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  18.5Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/longclust.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    libs   1.6Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scio’
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  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
Package suggested but not available for checking: ‘miceadds’
Note: found 55 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
'LazyData' is specified without a 'data' directory
installed size is 50.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  47.8Mb
'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
Error: package or namespace load failed for ‘LSTbook’:
 .onLoad failed in loadNamespace() for 'LSTbook', details:
  call: loadNamespace(name)
  error: there is no package called ‘ggformula’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rpostgis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   1.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘orthogene’
Package unavailable to check Rd xrefs: ‘orthogene’
Package suggested but not available for checking: ‘rnaturalearthhires’
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rlang’ ‘torch’
  All declared Imports should be used.
installed size is 31.6Mb
  sub-directories of 1Mb or more:
    libs  31.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quitte’
Package suggested but not available for checking: ‘SeqArray’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 55.5Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs  48.5Mb
'LazyData' is specified without a 'data' directory
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
Packages required and available but unsuitable versions:
  'parallel', 'stats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'pdInfoBuilder', 'oligo'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocCheck’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.3Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Namespaces in Imports field not imported from:
  ‘cli’ ‘nomnoml’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  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  10.5Mb
Note: found 55 marked UTF-8 strings
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  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 3058 marked UTF-8 strings
Note: found 11396 marked UTF-8 strings
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   3.5Mb
    libs         15.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    data   3.0Mb
    libs   4.6Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pbmcapply’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Note: found 5210 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      11.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘marssTMB’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.NCBI.GRCh38', 'wiggleplotr'
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.8Mb
'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 13.2Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.8Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
GNU make is a SystemRequirements.
qr.X: no visible binding for global variable ‘R’
Undefined global functions or variables:
  R
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 18 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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.9Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lars’ ‘methods’ ‘parallel’ ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  12.2Mb
Namespace in Imports field not imported from: ‘boot.heterogeneity’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  15.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  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
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'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:
    libs  10.7Mb
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: ‘cmdstanr’
installed size is 64.1Mb
  sub-directories of 1Mb or more:
    libs  62.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
ADPopSel: no visible global function definition for ‘%dorng%’
ADRand: no visible global function definition for ‘%dorng%’
ADSSMod: no visible global function definition for ‘%dorng%’
ADTreatSel: no visible global function definition for ‘%dorng%’
ClustRand: no visible global function definition for ‘%dorng%’
EventPred: no visible global function definition for ‘%dorng%’
FutRuleNCores: no visible global function definition for ‘%dorng%’
MultAdj1NCores: no visible global function definition for ‘%dorng%’
MultAdj2NCores: no visible global function definition for ‘%dorng%’
MultAdj3NCores: no visible global function definition for ‘%dorng%’
Undefined global functions or variables:
  %dorng%
Namespace in Imports field not imported from: ‘vroom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 123.6Mb
  sub-directories of 1Mb or more:
    libs  122.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.1Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    libs      3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘merlin.Rmd’ using rmarkdown

Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.4Mb
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 107.2Mb
  sub-directories of 1Mb or more:
    libs  106.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    help   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
Packages suggested but not available for checking:
  'hgu133a.db', 'hgu95av2.db'
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmerTest’
  All declared Imports should be used.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ade4’ ‘dendextend’ ‘ggforce’ ‘ggrepel’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 58.9Mb
  sub-directories of 1Mb or more:
    libs  58.5Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.8Mb
    libs  20.6Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.5Mb
Package required but not available: ‘qusage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘boot’ ‘energy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  17.0Mb
'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: ‘structSSI’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dada2’
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘utils’
  All declared Imports should be used.
Package required but not available: ‘microbiome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    lib    8.8Mb
    libs   4.4Mb
Found the following apparent S3 methods exported but not registered:
  plot.icss print.icss print.micss
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘midfielddata’
'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   6.0Mb
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
Package required but not available: ‘InteractiveComplexHeatmap’

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
installed size is 116.7Mb
  sub-directories of 1Mb or more:
    libs  116.0Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Package unavailable to check Rd xrefs: ‘mixAK’
Package required but not available: ‘dada2’

Packages suggested but not available for checking: 'ANCOMBC', 'mia'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   1.2Mb
    libs      1.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Packages suggested but not available for checking:
  'karyoploteR', 'regioneR'
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package which this enhances but not available for checking: ‘pbdMPI’
Package required but not available: ‘scran’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'smooth.construct.unc_pcre.smooth.spec' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ConfusionTableR’ ‘OddsPlotty’ ‘caret’ ‘dplyr’ ‘ggplot2’ ‘parsnip’
  ‘ranger’ ‘recipes’ ‘rsample’ ‘varhandle’ ‘workflows’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 237.0Mb
  sub-directories of 1Mb or more:
    include    9.6Mb
    libs     226.9Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
Namespaces in Imports field not imported from:
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  ‘htmltools’ ‘leaflet’ ‘lubridate’ ‘plotly’ ‘shinyjs’ ‘stringr’ ‘xts’
  ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘datasets’ ‘doParallel’ ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  15.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 92.7Mb
  sub-directories of 1Mb or more:
    libs  91.0Mb
'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 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'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:
    libs  10.4Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'doMPI', 'alstructure'

Package which this enhances but not available for checking: ‘MoBPSmaps’
Packages required but not available:
  'plyranges', 'RaggedExperiment', 'MultiAssayExperiment', 'ggbio'

Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR'

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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 18 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 5238 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    libs   4.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.1Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs     3.0Mb
    raster   2.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   2.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 68.9Mb
  sub-directories of 1Mb or more:
    libs  68.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  12.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Biostrings’
Package unavailable to check Rd xrefs: ‘Biostrings’
'LazyData' is specified without a 'data' directory
Note: found 75 marked UTF-8 strings
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   4.5Mb
    libs   3.5Mb
installed size is 45.2Mb
  sub-directories of 1Mb or more:
    libs  44.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following apparent S3 methods exported but not registered:
  plot.prevalence.msm plot.survfit.msm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘markdown’ ‘methods’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘mtvc-Ex.R’ failed
The error most likely occurred in:

> ### Name: mtvc
> ### Title: (mtvc) Multiple Time Varying Covariates
> ### Aliases: mtvc
> 
> ### ** Examples
> 
> data(simwide)
> cp.dataframe=mtvc(data=simwide,
+ origin='1970-01-01',
+ dates=c(FIRST_CHRONIC,FIRST_ACUTE,FIRST_RELAPSE),
+ complications=c(CHRONIC,ACUTE,RELAPSE),
+ start=DATETRAN,
+ stop=DLASTSE,
+ event=EVENT)
Error in `mutate()`:
ℹ In argument: `FIRST_CHRONIC = (structure(function (..., .x = ..1, .y =
  ..2, . = ..1) ...`.
Caused by error in `as.Date.numeric()`:
! 'origin' must be supplied
Backtrace:
     ▆
  1. ├─mtvc::mtvc(...)
  2. │ └─data %>% ungroup() %>% mutate(id = row_number()) %>% ...
  3. ├─dplyr::mutate_at(...)
  4. │ ├─dplyr::mutate(.tbl, !!!funs)
  5. │ └─dplyr:::mutate.data.frame(.tbl, !!!funs)
  6. │   └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  7. │     ├─base::withCallingHandlers(...)
  8. │     └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
  9. │       └─mask$eval_all_mutate(quo)
 10. │         └─dplyr (local) eval()
 11. ├─mtvc (local) `<inln_cl_>`(FIRST_CHRONIC)
 12. │ └─rlang::eval_bare(`_quo`, base::parent.frame())
 13. ├─rlang (local) as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 14. ├─base::as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 15. ├─base::as.Date.numeric(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 16. │ └─base::stop("'origin' must be supplied")
 17. └─base::.handleSimpleError(...)
 18.   └─dplyr (local) h(simpleError(msg, call))
 19.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9. │       └─mask$eval_all_mutate(quo)
   10. │         └─dplyr (local) eval()
   11. ├─mtvc (local) `<inln_cl_>`(FIRST_CHRONIC)
   12. │ └─rlang::eval_bare(`_quo`, base::parent.frame())
   13. ├─rlang (local) as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
   14. ├─base::as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
   15. ├─base::as.Date.numeric(ifelse(is.na(.), as.Date(origin), as.Date(.)))
   16. │ └─base::stop("'origin' must be supplied")
   17. └─base::.handleSimpleError(...)
   18.   └─dplyr (local) h(simpleError(msg, call))
   19.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
'LazyData' is specified without a 'data' directory
Found the following apparent S3 methods exported but not registered:
  plot.TetraDualStatis summary.TetraDualStatis
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GFDmcv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘plsgenomics’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is 106.9Mb
  sub-directories of 1Mb or more:
    libs  106.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Package suggested but not available for checking: ‘rrelaxiv’
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building ‘multipol.Rnw’ using Sweave
Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

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

    deriv

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

    single

Loading required package: polynom
Error: processing vignette 'multipol.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'multipol.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘multipol.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘poweRlaw’ ‘rmutil’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Note: found 6 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘cias.Rnw’ using Sweave

Attaching package: ‘multivator’

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

    levels, rbind

--- finished re-building ‘cias.Rnw’

--- re-building ‘multivator.Rnw’ using Sweave
Error: processing vignette 'multivator.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'multivator.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'multivator.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   7.0Mb
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
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'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   5.6Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘mlr3learners’ ‘rpart’
  All declared Imports should be used.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    22.9Mb
    models   1.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'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  6.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.7Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.5Mb
    libs   5.1Mb
GNU make is a SystemRequirements.
Note: found 140 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘rrpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'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:
    data   1.5Mb
    libs   4.2Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Note: found 7332 marked UTF-8 strings
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.5Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  17.3Mb
Package suggested but not available for checking: ‘fastshp’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.5Mb
Packages required and available but unsuitable versions: 'stats', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/networkscaleup.Rcheck/00install.out’ for details.
Note: found 2 marked Latin-1 strings
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Note: found 318 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nflfastR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'NGCHMDemoData', 'NGCHMSupportFiles'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHSRdatasets’ ‘grid’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    CppCode        3.5Mb
    R              8.1Mb
    classic-bugs   1.5Mb
    include       11.5Mb
    libs          17.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.7Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Package suggested but not available for checking: ‘doMPI’
'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:
    libs   8.9Mb
'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’
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’
  ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.1Mb
    mods   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
Found the following apparent S3 methods exported but not registered:
  print.fkk.test
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pedtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 20.7Mb
  sub-directories of 1Mb or more:
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    libs  14.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'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: ‘httr’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    doc       5.7Mb
    extdata   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.6Mb
    test_files   4.2Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.4Mb
    libs   3.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.9Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’ ‘ggthemes’ ‘mlbench’ ‘rmarkdown’ ‘tidymodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 99.2Mb
  sub-directories of 1Mb or more:
    libs  98.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.2Mb
  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  6.8Mb
  sub-directories of 1Mb or more:
    doc   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
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 842 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘crayon’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  44.0Mb
GNU make is a SystemRequirements.
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  40.1Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.6Mb
Note: found 34 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  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:
  ‘dplyr’ ‘glue’ ‘httpcode’ ‘httr’ ‘jsonlite’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    exampledata   1.5Mb
    libs          3.5Mb
GNU make is a SystemRequirements.
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    libs   20.9Mb
    share  10.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Note: found 2524 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 200.9Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    data      1.4Mb
    libs    189.3Mb
    models    4.7Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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    models   6.0Mb
Package suggested but not available for checking: ‘openNLPmodels.en’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.9Mb
Note: found 167 marked UTF-8 strings
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   8.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      4.6Mb
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs     33.6Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   6.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcplex’
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Namespaces in Imports field not imported from:
  ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'org.Dr.eg.db', 'scde'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    library   7.5Mb
Package which this enhances but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is 47.5Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs  43.9Mb
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
‘constparty.Rnw’... [3s/3s] OK
  ‘ctree.Rnw’ using ‘UTF-8’... [4s/4s] NOTE
differences from ‘ctree.Rout.save’
1409,1412d1408
< Deviance Residuals: 
<     Min       1Q   Median       3Q      Max  
< -45.801  -11.208   -1.049   10.903   53.615  
< 
  ‘mob.Rnw’... [5s/5s] OK
  ‘partykit.Rnw’... [1s/1s] OK
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.5Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘clusterProfiler’ ‘purrr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package required but not available: ‘Mfuzz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      7.4Mb
    help   3.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   3.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    help   3.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   3.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   3.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/pbdMPI.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

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
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.4Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    libs  24.5Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    help   1.4Mb
installed size is 133.1Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
    libs  129.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘PythonInR’
installed size is 21.1Mb
  sub-directories of 1Mb or more:
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    share  12.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ncvreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  14.0Mb
installed size is 134.4Mb
  sub-directories of 1Mb or more:
    libs  133.5Mb
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package suggested but not available for checking: ‘ptmixed’
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   7.0Mb
installed size is 56.2Mb
  sub-directories of 1Mb or more:
    libs  55.0Mb
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
'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
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  32.7Mb
GNU make is a SystemRequirements.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Note: found 114 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
installed size is 44.7Mb
  sub-directories of 1Mb or more:
    libs  43.9Mb
Package required but not available: ‘LBE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  46.4Mb
Warning in checkDepPackageVersion(dep_pkg = "Matrix", this_pkg = "TMB") :
  Package version inconsistency detected.
TMB was built with Matrix version 1.6.4
Current Matrix version is 1.6.5
Please re-install TMB from source or restore original ‘Matrix’ package (see '?reinstalling' for more information)

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.
Package suggested but not available for checking: ‘INLA’
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   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 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Package suggested but not available for checking: ‘slingshot’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   9.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Note: found 12992 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R             1.0Mb
    htmlwidgets   4.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘base’ ‘grDevices’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pmartRdata’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
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Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 62 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
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 21 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘formula.tools’ ‘ggplot2’ ‘gplots’ ‘graphics’ ‘purrr’
  ‘rstatix’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: ‘pollimetrydata’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    extdata   1.9Mb
'LazyData' is specified without a 'data' directory
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R      7.1Mb
    data   4.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.8Mb
    libs   1.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      2.9Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data      2.7Mb
    extdata   3.5Mb
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: ‘EmpiricalBrownsMethod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc  10.5Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’ ‘numDeriv’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    libs   8.5Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata  11.6Mb
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    data   2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   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 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
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installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinyApp   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   5.7Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    4.7Mb
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
installed size is 120.3Mb
  sub-directories of 1Mb or more:
    libs  119.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  35.0Mb
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   2.7Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.1Mb
Note: found 12717 marked UTF-8 strings
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’
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
Note: found 1 marked UTF-8 string
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is 130.2Mb
  sub-directories of 1Mb or more:
    libs  129.7Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.0Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Note: found 26 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 107 marked UTF-8 strings
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Package required but not available: ‘tweeDEseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.6Mb
installed size is  6.2Mb
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installed size is 51.3Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 31.6Mb
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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
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 16.5Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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Missing or unexported objects:
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  ‘async::when_all’
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  5.9Mb
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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
installed size is  5.3Mb
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installed size is 79.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 119.7Mb
  sub-directories of 1Mb or more:
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'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:
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘spDataLarge’
Namespaces in Imports field not imported from:
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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
installed size is  7.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘missMethods’
  All declared Imports should be used.
installed size is  5.1Mb
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installed size is 16.2Mb
  sub-directories of 1Mb or more:
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installed size is  8.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  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.
Note: found 6 marked UTF-8 strings
installed size is 12.6Mb
  sub-directories of 1Mb or more:
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    libs  11.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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installed size is 16.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
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installed size is  6.7Mb
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installed size is 11.5Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘MatrixModels’
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'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:
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installed size is  7.8Mb
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installed size is 10.6Mb
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installed size is  9.7Mb
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installed size is 10.7Mb
  sub-directories of 1Mb or more:
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> K_\text 
                   {max}
l.2230 ...to a user-specified \eqn{K_\text{max}}{}
                                                  )
! Undefined control sequence.
<argument> K_\text 
                   {max}
l.2256 ...er}{integer} scalar \eqn{K_\text{max}}{}
                                                  ,
! Undefined control sequence.
<argument> K^c+1=K_\text 
                         {max}
l.2282 ...is stopped if \eqn{K^c+1=K_\text{max}}{}
                                                  ,
Namespace in Imports field not imported from: ‘SparseM’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘fastshp’
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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installed size is 14.2Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘bootmlm’
installed size is  5.1Mb
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Namespace in Imports field not imported from: ‘magrittr’
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'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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installed size is 19.1Mb
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'library' or 'require' calls in package code:
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  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘BRugs’
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is 11.5Mb
  sub-directories of 1Mb or more:
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installed size is  7.3Mb
  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
Namespaces in Imports field not imported from:
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Package suggested but not available for checking: ‘slingshot’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 25.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.7Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 34.2Mb
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Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  5.8Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown
Quitting from lines 425-461 (ragtop_convertibles_in_r.Rmd) 
Error: processing vignette 'ragtop_convertibles_in_r.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘ragtop_convertibles_in_r.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 28.8Mb
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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 11.4Mb
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installed size is 11.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Spectra’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
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  All declared Imports should be used.
installed size is  7.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  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
Package suggested but not available for checking: ‘gurobi’
installed size is 16.6Mb
  sub-directories of 1Mb or more:
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'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:
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
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'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:
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'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 66.2Mb
  sub-directories of 1Mb or more:
    libs  65.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
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    etc    1.9Mb
    po     1.2Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
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installed size is 21.6Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘raybevel’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
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    libs   3.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘rex’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 57.1Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 58.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rhdf5’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rblpapi.Rcheck/00install.out’ for details.
installed size is 44.1Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26334 marked UTF-8 strings
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 66.1Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    cont  24.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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  8.6Mb
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installed size is  6.7Mb
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installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Packages suggested but not available for checking: 'ROntoTools', 'oligo'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rcplex.Rcheck/00install.out’ for details.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
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installed size is  6.5Mb
  sub-directories of 1Mb or more:
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installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      2.1Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    include  45.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 30.2Mb
  sub-directories of 1Mb or more:
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    libs     22.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
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installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
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    libs      4.9Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
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installed size is  7.3Mb
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installed size is  6.6Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
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'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
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.4Mb
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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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is  7.2Mb
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installed size is  8.8Mb
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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
installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘realTimeloads-Ex.R’ failed
The error most likely occurred in:

> ### Name: impute_data
> ### Title: Returns x with gaps imputed using ARIMA and Decision Trees,
> ###   optional uncertainty estimation using Monte Carlo resampling
> ### Aliases: impute_data
> 
> ### ** Examples
> 
> # Impute non-tidal data
> time <- realTimeloads::ExampleData$Sediment_Samples$time
> xo <- realTimeloads::ExampleData$Sediment_Samples$SSCxs_mg_per_liter
> Q <- realTimeloads::ExampleData$Discharge$Discharge_m_cubed_per_s
> idata <- sample(1:length(xo),round(length(xo)*0.5),replace=FALSE)
> x <- rep(NA,length(xo))
> x[idata] <- xo[idata] # simulated samples
> flow_concentrtion_ratio <- imputeTS::na_interpolation(Q/x)
> Xreg <- cbind(Q,flow_concentrtion_ratio)
> Output <- impute_data(time,x,Xreg,MC = 10,ptrain = 0.8)
Error in optim(init[mask], getLike, method = "L-BFGS-B", lower = rep(0,  : 
  L-BFGS-B needs finite values of 'fn'
Calls: impute_data -> <Anonymous> -> <Anonymous> -> optim
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.0Mb
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    libs   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
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Package suggested but not available for checking: ‘Rmpi’
installed size is 18.4Mb
  sub-directories of 1Mb or more:
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    libs  14.5Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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installed size is 11.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      4.6Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'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    3.4Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
'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  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.8Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  13.5Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs     19.5Mb
    models    1.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Package suggested but not available for checking: ‘ccdata’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RevGadgets’
'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
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  43.2Mb
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'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   5.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'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 27.9Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs   22.8Mb
'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
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  15.2Mb
installed size is  5.5Mb
  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
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_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.
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
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.4Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   8.7Mb
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 243 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/rJava.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    include   3.1Mb
    libs     19.0Mb
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 28.3Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  23.8Mb
'LazyData' is specified without a 'data' directory
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   16.4Mb
'LazyData' is specified without a 'data' directory
installed size is 103.5Mb
  sub-directories of 1Mb or more:
    libs  102.7Mb
GNU make is a SystemRequirements.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/rlibkriging.Rcheck/00install.out’ for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
'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  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RMark.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is 132.0Mb
  sub-directories of 1Mb or more:
    libs  131.6Mb
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 ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RmecabKo.Rcheck/00install.out’ for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ... (t+(r-1))\neq \mu (t+(s-1))\ \text 
                                                  {for some}\ t\in [0,1],\\ ...
l.380 \end{array}\right.}{}
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   5.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs       1.2Mb
    minizinc   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs  38.0Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rmpi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 61.8Mb
  sub-directories of 1Mb or more:
    libs  61.2Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
GNU make is a SystemRequirements.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Package suggested but not available for checking: ‘recount3’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
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 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'pbdMPI', 'Rmpi'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Packages unavailable to check Rd xrefs: ‘pbdMPI’, ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 101.0Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     98.8Mb
'LazyData' is specified without a 'data' directory
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R  11.4Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.3Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
Package suggested but not available for checking: ‘illuminaHumanv3.db’
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 86.5Mb
  sub-directories of 1Mb or more:
    libs  85.8Mb
GNU make is a SystemRequirements.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              5.0Mb
    simulationStudy   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'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   5.5Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    extdata   2.7Mb
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
sh: cmake: command not found
sh: cmake: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: cmake: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without 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 ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/ROracle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   5.4Mb
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs   7.7Mb
Warning in file(open = "w+") :
  cannot open file '/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpXYU41A/Rfab354374b02': No space left on device
Error in file(open = "w+") : cannot open the connection
Calls: <Anonymous> -> .load_package_quietly -> .try_quietly -> file
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 59.5Mb
  sub-directories of 1Mb or more:
    libs  58.3Mb
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  47.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /opt/R/arm64/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
  #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RQuantLib.Rcheck/00install.out’ for details.
installed size is 103.3Mb
  sub-directories of 1Mb or more:
    libs  102.7Mb
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespaces in Imports field not imported from:
  ‘keys’ ‘shinyWidgets’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  24.5Mb
'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’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 296.7Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 67.1Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 36.6Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 40.1Mb
  sub-directories of 1Mb or more:
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    libs  11.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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installed size is 36.5Mb
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Namespace in Imports field not imported from: ‘mc2d’
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installed size is 29.0Mb
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installed size is 22.3Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
installed size is 11.5Mb
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.0Mb
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installed size is  7.3Mb
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installed size is 99.8Mb
  sub-directories of 1Mb or more:
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installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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Running examples in ‘rtrend-Ex.R’ failed
The error most likely occurred in:

> ### Name: slope_rast
> ### Title: calculate slope of rast object
> ### Aliases: slope_rast rast_filter_time
> 
> ### ** Examples
> 
> library(rtrend)
> library(terra)
terra 1.7.71
> 
> f <- system.file("rast/MOD15A2_LAI_China_G050_2001-2020.tif", package = "rtrend")
> r <- rast(f)
> r
class       : SpatRaster 
dimensions  : 80, 140, 20  (nrow, ncol, nlyr)
resolution  : 0.5, 0.5  (x, y)
extent      : 70, 140, 15, 55  (xmin, xmax, ymin, ymax)
coord. ref. : lon/lat WGS 84 (EPSG:4326) 
source      : MOD15A2_LAI_China_G050_2001-2020.tif 
names       :      LAI,      LAI,      LAI,     LAI,      LAI,      LAI, ... 
min values  : 0.000000, 0.000000, 0.000000, 0.00000, 0.000000, 0.000000, ... 
max values  : 5.692542, 5.479348, 5.585326, 5.33587, 5.822826, 5.533152, ... 
time        : 978307200 to 1577836800 
> time(r)
 [1]  978307200 1009843200 1041379200 1072915200 1104537600 1136073600
 [7] 1167609600 1199145600 1230768000 1262304000 1293840000 1325376000
[13] 1356998400 1388534400 1420070400 1451606400 1483228800 1514764800
[19] 1546300800 1577836800
> 
> slp <- slope_rast(r,
+   period = c(2001, 2020), 
+   outfile = "LAI_trend.tif", overwrite = TRUE,
+   fun = rtrend::slope_mk, .progress = "none"
+ )
Error in as.POSIXlt.numeric(x, tz = tz(x)) : 'origin' must be supplied
Calls: slope_rast ... year -> year.default -> as.POSIXlt -> as.POSIXlt.numeric
Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test-slope_rast.R:9:3'): slope_rast works ───────────────────────────
  Error in `as.POSIXlt.numeric(x, tz = tz(x))`: 'origin' must be supplied
  Backtrace:
      ▆
   1. ├─rtrend::slope_rast(...) at test-slope_rast.R:9:3
   2. │ └─r %<>% rast_filter_time(period)
   3. └─rtrend::rast_filter_time(., period)
   4.   ├─lubridate::year(time(r))
   5.   └─lubridate:::year.default(time(r))
   6.     ├─base::as.POSIXlt(x, tz = tz(x))
   7.     └─base::as.POSIXlt.numeric(x, tz = tz(x))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 23 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘slope_rast.Rmd’ using rmarkdown

Quitting from lines 20-33 [setup] (slope_rast.Rmd)
Error: processing vignette 'slope_rast.Rmd' failed with diagnostics:
'origin' must be supplied
--- failed re-building ‘slope_rast.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  19.9Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 181.2Mb
  sub-directories of 1Mb or more:
    data    1.5Mb
    libs  178.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   2.5Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
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
Package which this enhances but not available for checking: ‘glmmADMB’
Package required but not available: ‘rWikiPathways’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    libs  43.9Mb
'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 63.3Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs     57.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    extdata   2.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Packages suggested but not available for checking:
  'BiocPkgTools', 'biocViews'
Packages unavailable to check Rd xrefs: ‘BiocPkgTools’, ‘biocViews’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.9Mb
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  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    libs  32.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
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installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.1Mb
    yacas   1.3Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs    8.8Mb
    yacas   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
'LazyData' is specified without a 'data' directory
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
installed size is 46.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  44.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   4.0Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'org.Sc.sgd.db'
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  46.7Mb
'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   4.9Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘gridExtra’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'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:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    bin   4.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   1.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \dfrac 
                       
l.192 ...omputed by  \eqn{\dfrac{|I|-ec}{|I|-1}}{}
                                                  .
! Undefined control sequence.
<argument> 1 - \dfrac 
                      {\hat {\ell }_{k,n}(1_I,0_{I^c})}{|I|}
l.280 ...ac{\hat{\ell}_{k,n}(1_I,0_{I^c})}{|I|}}{}
                                                  .
! Undefined control sequence.
<argument> S_I(\ell )=\dfrac 
                             {D_I(\ell )}{D(\ell )}
l.1278 ...{S_I(\ell)=\dfrac{D_I(\ell)}{D(\ell)}}{}
                                                  .
! Undefined control sequence.
<argument> S_I(\ell )=\dfrac 
                             {D_I(\ell )}{D(\ell )}
l.1364 ...{S_I(\ell)=\dfrac{D_I(\ell)}{D(\ell)}}{}
                                                  .
! Undefined control sequence.
<argument> \hat {S}_{I,k,n}=\dfrac 
                                   {\hat {D}_{I,k,n}}{\hat {D}_{k,n}}
l.1374 ...dfrac{\hat{D}_{I,k,n}}{\hat{D}_{k,n}}}{}
                                                  
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1607 ...hat{\Upsilon}_{I,k,n}}{\hat{D}_{k,n}}}{}
                                                   the empirical counterpart...
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1607 ...n{\dfrac{\Upsilon_I(\ell)}{D_I(\ell)}}{}
                                                  .
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1609 ... by \eqn{\dfrac{(2|I|+2)!}{2(|I|!)^2}}{}
                                                  .
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.6Mb
'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
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Packages suggested but not available for checking:
  'DropletUtils', 'Nebulosa'
Packages unavailable to check Rd xrefs: ‘DropletUtils’, ‘Nebulosa’
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   3.1Mb
Packages suggested but not available for checking: 'ontoProc', 'rrvgo'
'LazyData' is specified without a 'data' directory
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Package required but not available: ‘LoomExperiment’

Packages suggested but not available for checking:
  'scRNAseq', 'sceasy', 'SeuratDisk', 'SeuratWrappers',
  'zellkonverter', 'GEOfastq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required and available but unsuitable version: ‘UCell’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘scran’

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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RhpcBLASctl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'AUCell', 'decoupleR', 'infercnv', 'Nebulosa'
Package unavailable to check Rd xrefs: ‘infercnv’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘oligoClasses’
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘crayon’ ‘knitr’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 2 marked UTF-8 strings
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
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installed size is 61.3Mb
  sub-directories of 1Mb or more:
    libs  59.4Mb
'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   8.0Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  14.5Mb
GNU make is a SystemRequirements.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'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:
    data   2.9Mb
    libs   7.7Mb
Packages required but not available: 'ggmsa', 'msa'

Package suggested but not available for checking: ‘org.Rn.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rsbml’
Package suggested but not available for checking: ‘ArrayExpress’
Package unavailable to check Rd xrefs: ‘ArrayExpress’
Found the following apparent S3 methods exported but not registered:
  model.matrix.segmented model.matrix.stepmented vcov.stepmented
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘flowMerge’
Package unavailable to check Rd xrefs: ‘flowMerge’
Error(s) in re-building vignettes:
  ...
--- re-building ‘SEI_vignette.Rnw’ using knitr
Error: processing vignette 'SEI_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'SEI_vignette.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm8): Font bbm8 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SEI_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    www  34.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘webp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘editData’ ‘miniUI’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   2.4Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs    21.4Mb
    models   1.6Mb
Note: found 836 marked UTF-8 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.3Mb
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘widgetTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   1.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
'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: ‘BPCells’
Packages suggested but not available for checking:
  'BPCells', 'monocle', 'presto'
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   7.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
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installed size is  5.8Mb
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installed size is 261.3Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
installed size is  6.4Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/shide.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
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Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is  9.5Mb
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'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  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:
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  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 21.1Mb
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'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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installed size is 12.1Mb
  sub-directories of 1Mb or more:
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> X \in \mathbb 
                         {R}{n\times p}
l.3264 ...data \eqn{X \in \mathbb{R}{n\times p}}{}
                                                   such that its rows are
! Undefined control sequence.
<argument> ...Delta _{p-1} =\lbrace z \in \mathbb 
                                                  {R}^p~|~z_j > 0, \sum _{i=...
l.3267 }{}
           test whether the data is uniformly distributed.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1231 marked UTF-8 strings
Note: found 28 marked UTF-8 strings
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  5.5Mb
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Packages suggested but not available for checking:
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Packages unavailable to check Rd xrefs: ‘motifmatchr’, ‘TFBSTools’, ‘chromVAR’
Package suggested but not available for checking: ‘rhdf5’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
installed size is  5.9Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 18.6Mb
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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
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
     user  system elapsed 
    0.005   0.000   0.004 
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 154 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_bundle_sim.R:56:3'): bundle_sim() works for a simple DGP. ────
  res6$M not identical to mean(dat5$y).
  Objects equal but not identical
  ── Failure ('test_bundle_sim.R:67:3'): bundle_sim() works for a simple DGP. ────
  res8$M not identical to mean(ybar7).
  Objects equal but not identical
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 154 ]
  Error: Test failures
  Execution halted
installed size is  5.4Mb
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installed size is  6.3Mb
  sub-directories of 1Mb or more:
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installed size is  5.8Mb
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GNU make is a SystemRequirements.
installed size is 14.8Mb
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Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 22.3Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 12.0Mb
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installed size is  7.6Mb
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Packages suggested but not available for checking: 'graph', 'Rgraphviz'
Packages unavailable to check Rd xrefs: ‘Rgraphviz’, ‘graph’
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
installed size is 13.0Mb
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Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
installed size is  7.1Mb
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GNU make is a SystemRequirements.
installed size is 31.7Mb
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Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
installed size is  6.5Mb
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Note: found 23 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.7Mb
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.9Mb
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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
installed size is  9.4Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: ‘gurobi’
installed size is  5.7Mb
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GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
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'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:
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    libs   2.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SMITIDstruct’
installed size is  5.2Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.8Mb
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    libs  10.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Package which this enhances but not available for checking: ‘Rmpi’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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Package required but not available: ‘GWASTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘flextable’ ‘htmlTable’ ‘stringr’
  All declared Imports should be used.
Note: found 938 marked UTF-8 strings
installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [17s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected`: "0427" "1946"
  ── Failure ('test-audioblastProcessors.R:103:3'): .calcTimesOfDay() works as expected ──
  as.character(o[2, ]) (`actual`) not equal to c("2248", "0124") (`expected`).
  
  `actual`:   "2254" "0119"
  `expected`: "2248" "0124"
  ── Failure ('test-audioblastProcessors.R:105:3'): .calcTimesOfDay() works as expected ──
  as.character(o[4, ]) (`actual`) not equal to c("1206", "2248") (`expected`).
  
  `actual`:   "1207" "2254"
  `expected`: "1206" "2248"
  
  [ FAIL 18 | WARN 0 | SKIP 2 | PASS 828 ]
  Error: Test failures
  Execution halted
installed size is  7.6Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DropletUtils’
installed size is  5.9Mb
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installed size is 17.8Mb
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Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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installed size is  5.3Mb
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installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is 38.1Mb
  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
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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'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 16.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 35.2Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available:
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Package suggested but not available for checking: ‘bluster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
installed size is 54.6Mb
  sub-directories of 1Mb or more:
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  5.6Mb
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installed size is 13.0Mb
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GNU make is a SystemRequirements.
installed size is  6.0Mb
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GNU make is a SystemRequirements.
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Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.3Mb
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installed size is 22.5Mb
  sub-directories of 1Mb or more:
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installed size is 13.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘spDataLarge’
installed size is  6.6Mb
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installed size is  5.9Mb
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Note: found 34 marked UTF-8 strings
installed size is  8.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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installed size is  6.0Mb
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Undocumented S4 methods:
  generic '[' and siglist 'SpectraInTime,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTime,missing,ANY,ANY'
  generic '[' and siglist 'SpectraInTime,missing,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,ANY,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,missing,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  7.4Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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installed size is 22.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 17.2Mb
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installed size is 11.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    libs   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
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    extdata   2.6Mb
    libs     11.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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    libs   2.9Mb
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    1. ├─... %>% as_preview() at test-spork.R:297:1
    2. ├─spork::as_preview(.)
    3. └─spork:::as_preview.plotmath(.)
    4.   ├─latexpdf::as.png(...)
    5.   └─spork:::as.png.plotmath(...)
    6.     ├─ggplot2::ggplot(x, ...)
    7.     └─spork:::ggplot.plotmath(x, ...)
    8.       ├─ggplot2::ggplot(data.frame(x = 1, y = 1, label = (x)))
    9.       └─base::data.frame(x = 1, y = 1, label = (x))
   10.         ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
   11.         └─base::as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 101 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Note: found 199 marked UTF-8 strings
installed size is  7.1Mb
  sub-directories of 1Mb or more:
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installed size is 51.3Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘dbplyr’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    help   1.1Mb
    libs  10.9Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.4Mb
Namespaces in Imports field not imported from:
  ‘arm’ ‘brms’ ‘lme4’ ‘plotly’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  25.5Mb
'LazyData' is specified without a 'data' directory
installed size is 104.3Mb
  sub-directories of 1Mb or more:
    libs  103.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    lsndata   2.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scanstatistics’
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘mice’ ‘sandwich’ ‘zoo’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘stacomir.Rmd’ using rmarkdown

Quitting from lines 302-324 [rmmstd] (stacomir.Rmd)
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
duplicated values in No.pas
--- failed re-building ‘stacomir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 28.7Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
  ‘reshape2’ ‘stats’
  All declared Imports should be used.
installed size is 48.8Mb
  sub-directories of 1Mb or more:
    libs  48.4Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  11.6Mb
    lib       3.3Mb
GNU make is a SystemRequirements.
installed size is 90.0Mb
  sub-directories of 1Mb or more:
    libs  89.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘starsdata’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    1.7Mb
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.4Mb
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      4.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.2Mb
Namespaces in Imports field not imported from:
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  ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘readr’ ‘reshape2’ ‘rmarkdown’
  ‘shinydisconnect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.3Mb
Package suggested but not available for checking: ‘INLA’
installed size is 65.4Mb
  sub-directories of 1Mb or more:
    libs  64.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.4Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.2Mb
Malformed Title field: should not end in a period.
'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 34.7Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported objects:
  ‘GSVA::gsvaParam’ ‘GSVA::ssgseaParam’
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 139-147 [unnamed-chunk-5] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
'gsvaParam' is not an exported object from 'namespace:GSVA'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 78 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.3Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocParallel’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    2.2Mb
    libs   1.5Mb
installed size is 51.0Mb
  sub-directories of 1Mb or more:
    libs  49.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.3Mb
    doc    3.9Mb
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
installed size is 54.8Mb
  sub-directories of 1Mb or more:
    libs  54.2Mb
GNU make is a SystemRequirements.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    libs  44.0Mb
'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
Package suggested but not available for checking: ‘swephRdata’
'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   5.0Mb
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    libs  44.8Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘StackImpute’ ‘arm’ ‘boot’ ‘broom’ ‘knitr’ ‘mvtnorm’
  ‘randomForest’
  All declared Imports should be used.
'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   2.9Mb
    doc    1.8Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    fonts   1.7Mb
    libs   17.6Mb
'LazyData' is specified without a 'data' directory
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R         2.3Mb
    extdata   3.1Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 551 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘spork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 81 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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    libs   4.5Mb
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 301 marked UTF-8 strings
installed size is 14.9Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘microbiome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘reshape2’ ‘truncnorm’ ‘xtable’
  All declared Imports should be used.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument>  \text 
                  {logit} \big ( E(Y) \big ) = \tau + \alpha + \delta (r - 1), 
l.172 ...g ) = \tau + \alpha + \delta (r - 1), }{}
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    8.0Mb
    libs   1.7Mb
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Package which this enhances but not available for checking: ‘R2wd’
Package suggested but not available for checking: ‘MultiAssayExperiment’
Package suggested but not available for checking: ‘MultiAssayExperiment’
Unknown package ‘teal’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    4.5Mb
    help   2.7Mb
'LazyData' is specified without a 'data' directory
installed size is 293.7Mb
  sub-directories of 1Mb or more:
    R       3.1Mb
    libs  289.3Mb
installed size is 31.5Mb
  sub-directories of 1Mb or more:
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    libs       8.1Mb
    tessdata  22.2Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘mnlogit’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.0Mb
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
'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   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
'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
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    data   3.0Mb
Note: found 197527 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘readr’ ‘tidyverse’ ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 52.9Mb
  sub-directories of 1Mb or more:
    libs  52.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'filter.edsurvey.data.frame' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rblpapi’
Package unavailable to check Rd xrefs: ‘Rblpapi’
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SingleR’
Warning: declared S3 method 'filter.Seurat' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  43.8Mb
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   4.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘rrelaxiv’
installed size is 53.0Mb
  sub-directories of 1Mb or more:
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    tiledb  35.4Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘org.Rn.eg.db’
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 60.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  56.6Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
'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    2.2Mb
    libs   4.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    examples  12.2Mb
    include    3.6Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
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', 'tm.lexicon.GeneralInquirer'
'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:
    libs   5.0Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Packages required but not available: 'EnhancedVolcano', 'Mfuzz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 160 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: ‘gurobi’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
installed size is 211.7Mb
  sub-directories of 1Mb or more:
    R          6.1Mb
    help       1.6Mb
    include    1.8Mb
    libs     201.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data  13.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
installed size is 49.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  46.4Mb
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Package which this enhances but not available for checking: ‘fwelnet’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR', 'Capr'
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Packages required but not available: 'csaw', 'HiCDOC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘TreeDistData’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   2.3Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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    libs   3.2Mb
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    doc       1.3Mb
    extdata  14.8Mb
installed size is 121.2Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    libs  116.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  37.5Mb
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
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/triptych.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'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 33.6Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    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
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'transform.bal_oversampling' not found
Warning: declared S3 method 'transform.bal_subsampling' not found
Warning: declared S3 method 'transform.cla_fs' not found
Warning: declared S3 method 'transform.ts_aug_awareness' not found
Warning: declared S3 method 'transform.ts_aug_awaresmooth' not found
Warning: declared S3 method 'transform.ts_aug_flip' not found
Warning: declared S3 method 'transform.ts_aug_jitter' not found
Warning: declared S3 method 'transform.ts_aug_none' not found
Warning: declared S3 method 'transform.ts_aug_shrink' not found
Warning: declared S3 method 'transform.ts_aug_stretch' not found
Warning: declared S3 method 'transform.ts_aug_wormhole' not found
Warning: declared S3 method 'transform.ts_fil_ema' not found
Warning: declared S3 method 'transform.ts_fil_hp' not found
Warning: declared S3 method 'transform.ts_fil_kalman' not found
Warning: declared S3 method 'transform.ts_fil_lowess' not found
Warning: declared S3 method 'transform.ts_fil_ma' not found
Warning: declared S3 method 'transform.ts_fil_none' not found
Warning: declared S3 method 'transform.ts_fil_qes' not found
Warning: declared S3 method 'transform.ts_fil_recursive' not found
Warning: declared S3 method 'transform.ts_fil_seas_adj' not found
Warning: declared S3 method 'transform.ts_fil_ses' not found
Warning: declared S3 method 'transform.ts_fil_smooth' not found
Warning: declared S3 method 'transform.ts_fil_spline' not found
Warning: declared S3 method 'transform.ts_fil_winsor' not found
Warning: declared S3 method 'transform.ts_norm_none' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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  5.8Mb
  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
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 34 marked Latin-1 strings
'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
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    ubinc   2.0Mb
installed size is 106.5Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    doc     1.0Mb
    libs  103.1Mb
GNU make is a SystemRequirements.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
Note: found 2 marked UTF-8 strings
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       23.0Mb
'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   5.1Mb
'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      1.1Mb
    help   4.4Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is  9.5Mb
  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
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.4Mb
    libs  47.5Mb
GNU make is a SystemRequirements.
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
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
Package suggested but not available for checking: ‘USA.state.boundaries.data’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is 38.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  36.2Mb
Package required and available but unsuitable version: ‘utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  22.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is 271.2Mb
  sub-directories of 1Mb or more:
    extdata    2.8Mb
    libs     267.1Mb
'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
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      9.4Mb
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   7.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Missing link or links in documentation object 'bigamma.mckay.Rd':
  ‘[VGAM]{gammaff.mm}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    help   3.0Mb
Missing link or links in documentation object 'profilevglm.Rd':
  ‘[stats]{plot.profile}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 468 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘readr’ ‘uuid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.0Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 2754 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  49.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     29.5Mb
GNU make is a SystemRequirements.
installed size is 55.3Mb
  sub-directories of 1Mb or more:
    libs  54.9Mb
'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: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘changing_default_parameters.Rmd’ using rmarkdown
--- finished re-building ‘changing_default_parameters.Rmd’

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

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

Quitting from lines 68-71 [unnamed-chunk-2] (process_bouts.Rmd)
Error: processing vignette 'process_bouts.Rmd' failed with diagnostics:
'origin' must be supplied
--- failed re-building ‘process_bouts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 98.0Mb
  sub-directories of 1Mb or more:
    libs  96.7Mb
GNU make is a SystemRequirements.
'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  9.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   6.3Mb
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'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   5.7Mb
Note: found 3133 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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 29.4Mb
  sub-directories of 1Mb or more:
    libs  29.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.5Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Note: found 933 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
'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
installed size is 40.7Mb
  sub-directories of 1Mb or more:
    libs  39.8Mb
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  7.0Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    help   1.9Mb
    libs   1.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
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  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 54.1Mb
  sub-directories of 1Mb or more:
    libs  53.2Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    java  28.5Mb
'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
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘spork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 43.0Mb
  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 42.1Mb
  sub-directories of 1Mb or more:
    libs  41.8Mb
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  8.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   4.6Mb
Package suggested but not available for checking: ‘RNRCS’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
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
'LazyData' is specified without a 'data' directory
installed size is 40.6Mb
  sub-directories of 1Mb or more:
    libs  40.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
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 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
'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 12.6Mb
  sub-directories of 1Mb or more:
    include  12.5Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
'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
Found the following problems:
errorevol_ranking_vector_IW.Rd:68:38: Warning: nested emphasis <code>
'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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/adbcpostgresql.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  7.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.9Mb
    libs   1.2Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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   5.5Mb
'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
Package suggested but not available for checking: 'INLA'
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
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Encountered the following conversion/validation errors:
absindex.Rd:110: condition must be plain text
feemscatter.Rd:47: condition must be plain text
write.openfluor.Rd:43: condition must be plain text
'LazyData' is specified without 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 apparent S3 methods exported but not registered:
  print.amAlleleFreq print.amDataset summary.amCluster
  summary.amPairwise summary.amUnique
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
'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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
'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:
    documents     2.4Mb
    libs          1.1Mb
    screenshots   1.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.6Mb
    doc    1.7Mb
Package suggested but not available for checking: 'arcgisbinding'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/arcpbf.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
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  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    libs  37.1Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    bin   11.8Mb
    misc   2.1Mb
'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:
    include   6.5Mb
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
Package suggested but not available for checking: 'asteRiskData'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.1Mb
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
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 30.3Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/b64.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'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:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.6Mb
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:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
Package suggested but not available for checking: 'fdpbandsdata'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'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:
    java   9.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    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
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   5.4Mb
GNU make is a SystemRequirements.
'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 13.3Mb
  sub-directories of 1Mb or more:
    doc   10.8Mb
    libs   1.5Mb
Package suggested but not available for checking: 'INLA'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.8Mb
    libs   3.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    help   6.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.2Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'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  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.3Mb
    libs      1.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.0Mb
'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
GNU make is a SystemRequirements.
'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  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
installed size is 149.2Mb
  sub-directories of 1Mb or more:
    include  148.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ffbase'
Package suggested but not available for checking: 'INLA'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/bigrquerystorage.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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
Package suggested but not available for checking: 'vol2birdR'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
Running examples in 'bioRad-Ex.R' failed
The error most likely occurred in:

> ### Name: calculate_vp
> ### Title: Calculate a vertical profile ('vp') from a polar volume ('pvol')
> ###   file
> ### Aliases: calculate_vp
> 
> ### ** Examples
> 
> # Locate and read the polar volume example file
> pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
> 
> # Copy the file to a home directory with read/write permissions
> file.copy(pvolfile, "~/volume.h5")
[1] TRUE
> 
> # Calculate the profile
> vp <- calculate_vp("~/volume.h5")
Error in calculate_vp("~/volume.h5") : 
  The package "vol2birdR" is required to run `calculate_vp`.
Calls: calculate_vp -> <Anonymous>
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    doc    1.1Mb
    help   1.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      1.2Mb
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
GNU make is a SystemRequirements.
'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  8.0Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       5.1Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.2Mb
'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
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
Found the following significant warnings:
  bnlearn/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  inference/loglikelihood/../../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  inference/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  inference/rinterface/../../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  minimal/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  predict/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  sanitization/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.2/bnlearn.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  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      30.3Mb
GNU make is a SystemRequirements.
'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'
Error(s) in re-building vignettes:
--- re-building 'BOSO.Rmd' using rmarkdown

Quitting from lines 475-492 [plot_comparison_BOSOvsREST] (BOSO.Rmd)
Error: processing vignette 'BOSO.Rmd' failed with diagnostics:
The `legend.pos` theme element is not defined in the element hierarchy.
--- failed re-building 'BOSO.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(breakDown)
  > 
  > test_check("breakDown")
                               contribution
  (Intercept)                         0.240
  - satisfaction_level = 0.45        -0.049
  - number_project = 2                0.023
  - last_evaluation = 0.54            0.101
  - average_montly_hours = 135        0.354
  - time_spend_company = 3            0.323
  - salary = low                      0.006
  - sales = sales                     0.002
  - promotion_last_5years = 0         0.000
  - Work_accident = 0                 0.000
  final_prognosis                     1.000
  baseline:  0 
  [ FAIL 3 | WARN 12 | SKIP 0 | PASS 30 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_plot.R:38:3'): Output format ─────────────────────────────────
  plot(broken_rf_classif) has length 11, not length 9.
  ── Failure ('test_plot.R:39:3'): Output format ─────────────────────────────────
  plot(broken_lm_regr) has length 11, not length 9.
  ── Failure ('test_plot.R:40:3'): Output format ─────────────────────────────────
  plot(broken_glm_classif) has length 11, not length 9.
  
  [ FAIL 3 | WARN 12 | SKIP 0 | PASS 30 ]
  Error: Test failures
  Execution halted
'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: 'cmdstanr'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   3.6Mb
Package suggested but not available for checking: 'glmmADMB'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BRugs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.3Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    fonts   3.7Mb
    lib     4.5Mb
GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'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
'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
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  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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  7.4Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.1Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(canadianmaps)
  > 
  > test_check("canadianmaps")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-functions.R:14:3'): check-functions: scale_fill_map() returns a ggplot manual fill object ──
  output$scale_name (`actual`) not equal to "manual" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('manual')
  ── Failure ('test-functions.R:23:3'): check-functions: scale_color_map() returns a ggplot manual fill object ──
  output$scale_name (`actual`) not equal to "manual" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('manual')
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
'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: 'rnaturalearthhires'
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    www  12.1Mb
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   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
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc  19.9Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rkeops'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   1.7Mb
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 38.7Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
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
Package suggested but not available for checking: 'darts'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'countreg'
'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  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   2.2Mb
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  6.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
'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
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    libs   1.0Mb
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/clarabel.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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    extdata  48.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Found the following problems:
fitEmaxB.Rd:191:38: Warning: nested emphasis <code>
'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:
    doc   5.4Mb
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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tobit1'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Package suggested but not available for checking: 'PopGenome'
Package suggested but not available for checking: 'disttree'
'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'
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    R      1.0Mb
    libs   2.4Mb
'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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.0Mb
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: 'CAM'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
run_pipeline_gbq: no visible global function definition for
  'query_exec'
Undefined global functions or variables:
  query_exec
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: 'conosPanel', 'p2data'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
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
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.2Mb
    vignette_data   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   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
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
'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:
[1] -0.06720261

$mu_normalNB
          [,1]
[1,] 0.2310491

$variance
           [,1]
[1,] 0.05666667

> 
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  10.45 0.15 10.72 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  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   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
'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:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer3'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'EnsDb.Hsapiens.v86'
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without 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   3.8Mb
    doc    1.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   7.7Mb
installed size is  7.5Mb
  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
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: 'IRanges'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  ./src/common/stddecl.h:481:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.2/cubature.Rcheck/00install.out' for details.
'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    1.8Mb
    libs   5.8Mb
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  6.4Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    libs   1.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'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   4.9Mb
'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
Package which this enhances but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
str:
  function(object, ...)
str.language:
  function(expr, name, indent)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

Found the following apparent S3 methods exported but not registered:
  str.language
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
'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
Running examples in 'dartR-Ex.R' failed
The error most likely occurred in:

> ### Name: gl.pcoa.plot
> ### Title: Bivariate or trivariate plot of the results of an ordination
> ###   generated using gl.pcoa()
> ### Aliases: gl.pcoa.plot
> 
> ### ** Examples
> 
>  test <- gl.pcoa(platypus.gl)
Starting gl.pcoa 
  Processing genlight object with SNP data
  Warning: data include loci that are scored NA across all individuals.
  Consider filtering using gl <- gl.filter.allna(gl)
  Performing a PCA, individuals as entities, loci as attributes, SNP genotype as state
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
GNU make is a SystemRequirements.
Packages required and available but unsuitable versions: 'utils', 'methods'

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
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:
> 
> ### Name: update_dev_pkg
> ### Title: Perform update of development version of a package
> ### Aliases: update_dev_pkg
> ### Keywords: data
> 
> ### ** Examples
> 
> ## Don't show: 
>  # using if(FALSE) because \dontrun could still be run by  --run-dontrun; #5421 
> ## End(Don't show)
>   if (FALSE) data.table::update_dev_pkg()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  8.14 0.21 9.34 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: 'SASxport'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: 'BRugs'
Package suggested but not available for checking: 'INLA'
'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
'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:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    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  6.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
    libs   1.2Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
'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          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
'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  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
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'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
Package suggested but not available for checking: 'INLA'
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
Package which this enhances but not available for checking: 'INLA'
'LazyData' is specified without 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
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 17.0Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
'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 'introduction_to_dnapath.Rmd' using rmarkdown

Quitting from lines 221-224 [unnamed-chunk-8] (introduction_to_dnapath.Rmd)
Error: processing vignette 'introduction_to_dnapath.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
--- failed re-building 'introduction_to_dnapath.Rmd'

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

Quitting from lines 234-239 [unnamed-chunk-17] (package_data.Rmd)
Error: processing vignette 'package_data.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
--- failed re-building 'package_data.Rmd'

SUMMARY: processing the following files failed:
  'introduction_to_dnapath.Rmd' 'package_data.Rmd'

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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.1Mb
'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(docxtools)
  > 
  > test_check("docxtools")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 22 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_put.R:21:3'): put_axes() attributes match expectations ───────
  p$layers[[1]]$geom$non_missing_aes not identical to c("linetype", "linewidth", "shape").
  Lengths differ: 2 is not 3
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 22 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.7Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'gurobi'
'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
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Unknown package 'broomExtra' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/DRviaSPCN.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Package suggested but not available for checking: 'dsBaseClient'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    htmlwidgets   5.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
'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
Package suggested but not available for checking: 'cmdstanr'
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    data   9.0Mb
Package unavailable to check Rd xrefs: 'cmdstanr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lle'
'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   2.5Mb
    doc    1.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    bin       3.5Mb
    extdata   1.7Mb
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
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without 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 'convergence_problems.Rmd' using rmarkdown
--- finished re-building 'convergence_problems.Rmd'

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

Quitting from lines 373-374 [unnamed-chunk-35] (introduction_EcoDiet.Rmd)
Error: processing vignette 'introduction_EcoDiet.Rmd' failed with diagnostics:
The `legend.byrow` theme element must be a <logical> object.
--- failed re-building 'introduction_EcoDiet.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'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
Package suggested but not available for checking: 'lavaan.survey'
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'eggCountsExtra'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
GNU make is a SystemRequirements.
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eiCompare)
  Loading required package: eiPack
  Loading required package: ei
  Loading required package: wru
  
  Please cite as:
  
  Khanna K, Bertelsen B, Olivella S, Rosenman E, Rossell Hayes A, Imai K
  (2024). _wru: Who are You? Bayesian Prediction of Racial Category Using
  Surname, First Name, Middle Name, and Geolocation_. R package version
  3.0.0, <https://CRAN.R-project.org/package=wru>.
  
  Note that wru 2.0.0 uses 2020 census data by default.
  Use the argument `year = "2010"`, to replicate analyses produced with earlier package versions.
  
  > 
  > test_check("eiCompare")
  Error in wru::predict_race(voter.file = wru_voter_file, census.surname = use_surname,  : 
    unused argument (surname.year = surname_year)
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 75 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_wru_predict_race_wrapper.R:19:3'): WRU wrapper correctly calculates probabilities. ──
  Error in `if (grep("cannot open the connection", error_type$message)) {
      message("Failed to connect to the remote data sources. Check internet connection. Returning NULL")
      return()
  } else {
      stop()
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─eiCompare::wru_predict_race_wrapper(...) at test_wru_predict_race_wrapper.R:19:3
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 75 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'bisg.Rmd' using rmarkdown

Quitting from lines 127-149 [unnamed-chunk-13] (bisg.Rmd)
Error: processing vignette 'bisg.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'bisg.Rmd'

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

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

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

Quitting from lines 166-191 [apply_bisg] (performance_analysis.Rmd)
Error: processing vignette 'performance_analysis.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'performance_analysis.Rmd'

SUMMARY: processing the following files failed:
  'bisg.Rmd' 'performance_analysis.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
'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:
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
'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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (5) ePCR.Rd:0-17: Must have a \description
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   2.5Mb
Package suggested but not available for checking: 'epidict'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
    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
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(epos)
  > 
  > test_check("epos")
  [ FAIL 1 | WARN 12 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_createTanimotoBaseline.R:39:3'): Test function createTanimotoBaseline() ──
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 11 - 9 == 2
  Backtrace:
      ▆
   1. └─testthat::expect_that(length(tanimotobaseline), equals(9)) at test_createTanimotoBaseline.R:39:3
   2.   └─testthat (local) condition(object)
   3.     └─testthat::expect_equal(x, expected, ..., expected.label = label)
  
  [ FAIL 1 | WARN 12 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    doc  13.3Mb
'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  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ExactData'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    exiftool  14.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cec2013'
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.7Mb
GNU make is a SystemRequirements.
'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
Package suggested but not available for checking: 'exuberdata'
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
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.0Mb
    help   1.1Mb
'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
GNU make is a SystemRequirements.
installed size is  5.1Mb
  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
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    help   1.7Mb
    libs   1.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.1Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'coxKM'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    Rcgi      3.1Mb
    cgi-bin   2.9Mb
.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
Package suggested but not available for checking: 'NNLM'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/fcl.Rcheck/00install.out' for details.
'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  7.5Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
    libs   1.6Mb
Unexported object imported by a ':::' call: 'fdapace:::interp2lin'
  See the note in ?`:::` about the use of this operator.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'feasts.Rmd' using rmarkdown

Quitting from lines 49-51 [season-plot] (feasts.Rmd)
Error: processing vignette 'feasts.Rmd' failed with diagnostics:
`breaks` and `labels` have different lengths.
--- failed re-building 'feasts.Rmd'

SUMMARY: processing the following file failed:
  'feasts.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
'LazyData' is specified without 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      1.9Mb
    extdata   2.8Mb
    libs      1.1Mb
Package suggested but not available for checking: 'MicrobeDS'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    3.0Mb
    help   1.1Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R         4.7Mb
    doc       2.1Mb
    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  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'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
Package suggested but not available for checking: 'diveRsity'
Unknown package 'diveRsity' in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
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  5.7Mb
  sub-directories of 1Mb or more:
    lib    3.0Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Package suggested but not available for checking: 'gridlayout'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fivethirtyeightdata'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
Found the following apparent S3 methods exported but not registered:
  plot.fpp
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    3.6Mb
    libs   1.6Mb
'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    1.9Mb
    help   2.3Mb
    libs   1.2Mb
'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 23.5Mb
  sub-directories of 1Mb or more:
    libs  22.4Mb
GNU make is a SystemRequirements.
'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:
    doc    9.1Mb
    libs   1.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'fmeffects-Ex.R' failed
The error most likely occurred in:

> ### Name: ForwardMarginalEffect
> ### Title: R6 Class representing a forward marginal effect (FME)
> ### Aliases: ForwardMarginalEffect
> 
> ### ** Examples
> 
> 
> ## ------------------------------------------------
> ## Method `ForwardMarginalEffect$new`
> ## ------------------------------------------------
> 
> 
> # Train a model:
> 
> library(mlr3verse)
Loading required package: mlr3
> library(ranger)
> data(bikes, package = "fmeffects")
> forest = lrn("regr.ranger")$train(as_task_regr(x = bikes, id = "bikes", target = "count"))
> 
> # Create an `ForwardMarginalEffect` object:
> effects = ForwardMarginalEffect$new(makePredictor(forest, bikes, "count"),
+                   feature = c("temp", "humidity"),
+                   step.size = c(1, 0.01),
+                   ep.method = "envelope")
> 
> ## ------------------------------------------------
> ## Method `ForwardMarginalEffect$compute`
> ## ------------------------------------------------
> 
> # Compute results:
> effects$compute()
> 
> ## ------------------------------------------------
> ## Method `ForwardMarginalEffect$plot`
> ## ------------------------------------------------
> 
> # Compute results:
> effects$plot()
Warning in ggplot2::geom_segment(ggplot2::aes(x = (0.5 * min(x1) + 0.5 *  :
  All aesthetics have length 1, but the data has 699 rows.
ℹ Did you mean to use `annotate()`?
Warning in ggplot2::geom_segment(ggplot2::aes(y = (0.5 * min(x2) + 0.5 *  :
  All aesthetics have length 1, but the data has 699 rows.
ℹ Did you mean to use `annotate()`?
Error in as.vector(x, "character") : 
  cannot coerce type 'environment' to vector of type 'character'
Calls: <Anonymous> ... validDetails.text -> as.character -> as.character.default
Execution halted
Error(s) in re-building vignettes:
--- re-building 'fme_theory.Rmd' using rmarkdown
--- finished re-building 'fme_theory.Rmd'

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

Quitting from lines 92-100 [unnamed-chunk-7] (fmeffects.Rmd)
Error: processing vignette 'fmeffects.Rmd' failed with diagnostics:
cannot coerce type 'environment' to vector of type 'character'
--- failed re-building 'fmeffects.Rmd'

SUMMARY: processing the following file failed:
  'fmeffects.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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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   2.7Mb
    doc    1.1Mb
    libs   1.1Mb
'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: 'RandomFields'
'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:
    R      1.2Mb
    help   2.2Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.8Mb
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
GNU make is a SystemRequirements.
Found the following significant warnings:

  Warning: 'lwgeom::st_perimeter' is deprecated.
  Warning: 'lwgeom::st_perimeter' is deprecated.
  Warning: 'lwgeom::st_perimeter' is deprecated.
  Warning: 'lwgeom::st_perimeter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   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
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    doc   31.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.8Mb
'LazyData' is specified without a 'data' directory
'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.
Package suggested but not available for checking: 'paleofire'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 77.5Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
    libs     60.1Mb
    proj      8.2Mb
installed size is 76.1Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     2.8Mb
    libs    62.1Mb
    proj     7.7Mb
installed size is 73.6Mb
  sub-directories of 1Mb or more:
    gdal   2.8Mb
    libs  60.8Mb
    proj   7.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.2Mb
    libs      1.1Mb
'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
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 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   3.5Mb
Package suggested but not available for checking: 'geomarocdata'
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R         9.6Mb
    extdata   2.5Mb
    help      2.4Mb
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(geomtextpath)
  Loading required package: ggplot2
  > 
  > test_check("geomtextpath")
  [ FAIL 1 | WARN 7 | SKIP 3 | PASS 460 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-text_helpers.R:30:3', 'test-utils.R:215:3'
  • utils.R has been moved (1): 'test-utils.R:275:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-coord_curvedpolar.R:76:3'): wrapping first and last labels works as expected ──
  make_label(axis_labels$textpath$label[[9]]$glyph) (`actual`) not identical to expression(paste(1, "/", 10)) (`expected`).
  
  `actual[[1]]`:   `paste(1L, "/", 10L)`
  `expected[[1]]`: `paste(1, "/", 10)`  
  
  [ FAIL 1 | WARN 7 | SKIP 3 | PASS 460 ]
  Error: Test failures
  Execution halted
'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: 'RandomFields'

Package which this enhances but not available for checking: 'INLA'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RGtk2'
'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)
  > test_check("gfpop")
  Loading required package: gfpop
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 40 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-sn.R:3:1'): (code run outside of `test_that()`) ────────────────
  <install_error/error/condition>
  Error: Failed to install 'unknown package' from GitHub:
    HTTP error 403.
    API rate limit exceeded for 129.217.207.166. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)
  
    Rate limit remaining: 0/60
    Rate limit reset at: 2024-02-26 15:20:30 UTC
  
    To increase your GitHub API rate limit
    - Use `usethis::create_github_token()` to create a Personal Access Token.
    - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`.
  Backtrace:
      ▆
   1. └─devtools::install_github("vrunge/gfpop.data") at test-sn.R:3:1
   2.   ├─pkgbuild::with_build_tools(...)
   3.   │ └─pkgbuild:::withr_with_path(rtools_path(), code)
   4.   │   └─base::force(code)
   5.   └─remotes:::install_remotes(...)
   6.     └─base::tryCatch(...)
   7.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   8.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 40 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      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:
    doc    6.6Mb
    help   1.1Mb
'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
Running examples in 'gghdr-Ex.R' failed
The error most likely occurred in:

> ### Name: geom_hdr_boxplot
> ### Title: Box plot for the highest density region
> ### Aliases: geom_hdr_boxplot
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> ggplot(faithful, aes(y = eruptions)) +
+   geom_hdr_boxplot()
Warning: The dot-dot notation (`..prob..`) was deprecated in ggplot2 3.4.0.
ℹ Please use `after_stat(prob)` instead.
Warning: The following aesthetics were dropped during statistical transformation: y.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
  the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
  variable into a factor?
Warning: The `scale_name` argument of `discrete_scale()` is deprecated as of ggplot2
3.5.0.
Warning: The S3 guide system was deprecated in ggplot2 3.5.0.
ℹ It has been replaced by a ggproto system that can be extended.
Error in if (guide$reverse) { : argument is of length zero
Calls: <Anonymous> ... <Anonymous> -> train -> guide_train -> guide_train.prob_guide
Execution halted
Error(s) in re-building vignettes:
--- re-building 'gghdr.Rmd' using rmarkdown

Quitting from lines 93-98 [setup] (gghdr.Rmd)
Error: processing vignette 'gghdr.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'gghdr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   7.0Mb
'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  5.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.3Mb
    help   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
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.4Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'ggprism-Ex.R' failed
The error most likely occurred in:

> ### Name: annotation_ticks
> ### Title: Add ticks as ggplot annotation
> ### Aliases: annotation_ticks
> 
> ### ** Examples
> 
> ## Generally it is better to use the guide_prism_minor function.
> ## However annotation_ticks is useful in a few specific situations.
> library(ggplot2)
> 
> ## easily put ticks without labels around a plot with a border
> ggplot(mtcars, aes(x = mpg, y = disp)) +
+   geom_point() +
+   theme_prism(border = TRUE) +
+   coord_cartesian(clip = "off") +
+   annotation_ticks(sides = "tr", type = "major", outside = TRUE) +
+   theme(plot.margin = unit(c(4, 4, 4, 4), "mm"))
Error in `plot_theme()`:
! The `legend.text.align` theme element is not defined in the element
  hierarchy.
Backtrace:
     ▆
  1. ├─base (local) `<fn>`(x)
  2. └─ggplot2:::print.ggplot(x)
  3.   ├─ggplot2::ggplot_gtable(data)
  4.   └─ggplot2:::ggplot_gtable.ggplot_built(data)
  5.     └─ggplot2:::plot_theme(plot)
  6.       └─ggplot2:::validate_theme(theme)
  7.         └─base::mapply(...)
  8.           └─ggplot2 (local) `<fn>`(...)
  9.             └─cli::cli_abort(...)
 10.               └─rlang::abort(...)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'axes.Rmd' using rmarkdown

Quitting from lines 38-48 [unnamed-chunk-2] (axes.Rmd)
Error: processing vignette 'axes.Rmd' failed with diagnostics:
<Guide> classes have been rewritten as <ggproto> classes.
The old S3 guide methods have been superseded.
--- failed re-building 'axes.Rmd'

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

Quitting from lines 44-51 [unnamed-chunk-2] (colours.Rmd)
Error: processing vignette 'colours.Rmd' failed with diagnostics:
The `legend.text.align` theme element is not defined in the element
hierarchy.
--- failed re-building 'colours.Rmd'

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

Quitting from lines 45-59 [unnamed-chunk-2] (ggprism.Rmd)
Error: processing vignette 'ggprism.Rmd' failed with diagnostics:
The `legend.text.align` theme element is not defined in the element
hierarchy.
--- failed re-building 'ggprism.Rmd'

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

Quitting from lines 66-74 [unnamed-chunk-3] (pvalues.Rmd)
Error: processing vignette 'pvalues.Rmd' failed with diagnostics:
The `legend.text.align` theme element is not defined in the element
hierarchy.
--- failed re-building 'pvalues.Rmd'

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

Quitting from lines 53-63 [unnamed-chunk-3] (themes.Rmd)
Error: processing vignette 'themes.Rmd' failed with diagnostics:
The `legend.text.align` theme element is not defined in the element
hierarchy.
--- failed re-building 'themes.Rmd'

SUMMARY: processing the following files failed:
  'axes.Rmd' 'colours.Rmd' 'ggprism.Rmd' 'pvalues.Rmd' 'themes.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  5.9Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
'LazyData' is specified without a 'data' directory
Running examples in 'ggstatsplot-Ex.R' failed
The error most likely occurred in:

> ### Name: ggscatterstats
> ### Title: Scatterplot with marginal distributions and statistical results
> ### Aliases: ggscatterstats
> 
> ### ** Examples
> 
> set.seed(123)
> 
> # creating a plot
> p <- ggscatterstats(
+   iris,
+   x = Sepal.Width,
+   y = Petal.Length,
+   label.var = Species,
+   label.expression = Sepal.Length > 7.6
+ ) +
+   ggplot2::geom_rug(sides = "b")
> 
> # looking at the plot
> p
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in guide$position : object of type 'closure' is not subsettable
Calls: <Anonymous> ... panel_guides_grob -> %||% -> guide_for_position -> vapply -> FUN
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/ggtern.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    9.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ghibli)
  > 
  > test_check("ghibli")
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 8 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-scales.R:40:3'): scale_colour_ghibli_d fails as expected ─────
  `base_color_plot + scale_colour_ghibli_d()` did not throw an error.
  ── Failure ('test-scales.R:67:3'): scale_fill_ghibli_d fails as expected ───────
  `base_fill_plot + scale_fill_ghibli_d()` did not throw an error.
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 8 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    Giac  17.9Mb
GNU make is a SystemRequirements.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/gifski.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   2.5Mb
'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:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
'LazyData' is specified without a 'data' directory
Running 'spelling.R' [0s]
  Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(glancedata)
  > 
  > test_check("glancedata")
  [ FAIL 5 | WARN 4 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot_numerical_vars.R:7:3'): histogram mode is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:14:3'): density is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:22:3'): boxplot is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:30:3'): violin is a list of length 9 ───
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:37:3'): qqplot is a list of length 9 ───
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 5 | WARN 4 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    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.
GNU make is a SystemRequirements.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
GNU make is a SystemRequirements.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc             1.4Mb
    libs            4.5Mb
    test_data       2.2Mb
    vignette_data   1.2Mb
'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
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Found the following problems:
get_k_stages_adjacency_tensor.Rd:58:38: Warning: nested emphasis <code>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    R   6.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.5Mb
'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
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:
    help   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  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.0Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
Package suggested but not available for checking: 'doMC'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.7Mb
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  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
'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  5.9Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following problems:
GWASinlps.Rd:187:1: Warning: trimming empty <h4>
'LazyData' is specified without 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 267.7Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    java  264.7Mb
'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    1.0Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
    doc     4.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    2.6Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
Found the following problems:
KMHFA.Rd:128:38: Warning: nested emphasis <code>


KMHFA.Rd:132:38: Warning: nested emphasis <code>


KPCA.Rd:73:38: Warning: nested emphasis <code>


KPCA.Rd:77:38: Warning: nested emphasis <code>


KPE.Rd:83:38: Warning: nested emphasis <code>


KPE.Rd:87:38: Warning: nested emphasis <code>
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.3Mb
'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  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
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:
    doc   5.1Mb
'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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    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: 'INLA'
'LazyData' is specified without 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: 'trackr'
Package which this enhances but not available for checking: 'HadoopStreaming'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.3Mb
html_describe_con: multiple local function definitions for 'g' 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
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   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  6.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    help   1.1Mb
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
Package suggested but not available for checking: 'hurricaneexposuredata'
'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: 'microViz'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
Found the following problems:
baseflow.Rd:167:38: Warning: nested emphasis <code>


baseflow.Rd:171:38: Warning: nested emphasis <code>
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
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
Found the following problems:
KIALS.Rd:92:38: Warning: nested emphasis <code>


KIALS.Rd:96:38: Warning: nested emphasis <code>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SparkR'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.6Mb
    libs   1.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'iccCounts_examples.Rmd' using rmarkdown

Quitting from lines 92-93 [unnamed-chunk-6] (iccCounts_examples.Rmd)
Error: processing vignette 'iccCounts_examples.Rmd' failed with diagnostics:
Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `scales_add_defaults()`:
! could not find function "scales_add_defaults"
--- failed re-building 'iccCounts_examples.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'icd'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.2Mb
    help   1.8Mb
    libs   6.4Mb
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 11.4Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         1.4Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.0Mb
    libs      9.8Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    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
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
GNU make is a SystemRequirements.
logLik:
  function(object, ...)
logLik.displacement:
  function(model, ...)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

Found the following apparent S3 methods exported but not registered:
  logLik.displacement
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
S3 methods shown with full name in documentation object 'logLik.displacement':
  'logLik.displacement'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'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: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
'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
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
Running 'testthat.R' [93s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(inTextSummaryTable)
  > 
  > test_check("inTextSummaryTable")
  [ FAIL 2 | WARN 167 | SKIP 0 | PASS 991 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_subjectProfileSummaryPlot-general.R:25:2'): The plot is correctly facetted based on a variable ──
  `... <- NULL` produced warnings.
  ── Failure ('test_subjectProfileSummaryPlot-table.R:356:2'): The size of the points (in the legend) is correctly set ──
  gg$guides$colour$override.aes$size not equal to `pointSize`.
  target is NULL, current is numeric
  
  [ FAIL 2 | WARN 167 | SKIP 0 | PASS 991 ]
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/intrinsicFRP.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'surveyspec'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(iperform)
  > 
  > test_check("iperform")
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 45 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-dday.R:7:3'): dday works ─────────────────────────────────────
  dday(df, "2023-08-03", x = "x") (`actual`) not identical to 8 (`expected`).
  
    `actual`: 0
  `expected`: 8
  ── Failure ('test-dday.R:8:3'): dday works ─────────────────────────────────────
  dday(df, "2023-08-05", d = -1, x = "x") (`actual`) not identical to 12 (`expected`).
  
    `actual`:  0
  `expected`: 12
  ── Failure ('test-dday.R:9:3'): dday works ─────────────────────────────────────
  dday(df, "2023-08-05", d = 0, x = "x") (`actual`) not identical to 6 (`expected`).
  
    `actual`: 0
  `expected`: 6
  ── Failure ('test-dday.R:10:3'): dday works ────────────────────────────────────
  dday(df, "2023-08-01", d = 1, x = "x") (`actual`) not identical to 13 (`expected`).
  
    `actual`:  0
  `expected`: 13
  ── Failure ('test-ytd.R:12:3'): ytd works ──────────────────────────────────────
  ytd(df, "2023-08-01", x = "x") (`actual`) not equal to dday(df, "2023-08-01", x = "x") (`expected`).
  
    `actual`: 10
  `expected`:  0
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 45 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    data   1.9Mb
    doc    2.3Mb
    libs   3.1Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'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'
'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:
    art_profiles   1.5Mb
    libs           9.0Mb
GNU make is a SystemRequirements.
'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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   3.4Mb
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    i18n   6.5Mb
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'remMap'
'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/4.2/journalabbr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   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
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    help   6.6Mb
'LazyData' is specified without a 'data' directory
apparently using $(BLAS_LIBS) without following $(FLIBS) in 'src/Makevars'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Package suggested but not available for checking: 'RGeostats'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  '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
'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  6.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   1.7Mb
'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  6.5Mb
  sub-directories of 1Mb or more:
    doc   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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.5Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   4.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rsyslog'
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.7Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.0Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
> 
> # okay
> lint(
+   text = "expect_equal(x, 2)",
+   linters = yoda_test_linter()
+ )
> 
> lint(
+   text = 'expect_identical(x, "a")',
+   linters = yoda_test_linter()
+ )
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  213.14 89.86 314.14 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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs       1.4Mb
    testdata   1.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R              1.2Mb
    doc-software   2.4Mb
Error(s) in re-building vignettes:
--- re-building 'LMoFit.Rmd' using rmarkdown

Quitting from lines 236-237 [unnamed-chunk-15] (LMoFit.Rmd)
Error: processing vignette 'LMoFit.Rmd' failed with diagnostics:
Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `scales_add_defaults()`:
! could not find function "scales_add_defaults"
--- failed re-building 'LMoFit.Rmd'

SUMMARY: processing the following file failed:
  'LMoFit.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: 'EnsDb.Hsapiens.v75'
Package suggested but not available for checking: 'rsyslog'
Package suggested but not available for checking: 'rsyslog'
'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/4.2/longclust.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
Found the following significant warnings:
  Warning: replacing previous import 'ggmulti::coord_radial' by 'ggplot2::coord_radial' when loading 'loon.ggplot'
See 'd:/Rcompile/CRANpkg/local/4.2/loon.ggplot.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'scio'
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  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      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
Package suggested but not available for checking: 'kerdiest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  5.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.1Mb
Package suggested but not available for checking: 'depth'
'LazyData' is specified without a 'data' directory
installed size is 71.4Mb
  sub-directories of 1Mb or more:
    gdal   2.8Mb
    libs  60.7Mb
    proj   7.7Mb
'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: 'rnaturalearthhires'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'lpjmlkit', 'quitte'
Package suggested but not available for checking: 'doMC'
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs  36.3Mb
'LazyData' is specified without a 'data' directory
Packages required and available but unsuitable versions:
  'parallel', 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'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 10.0Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   3.5Mb
    libs          3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs       1.3Mb
'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: 'marssTMB'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BSgenome.Hsapiens.NCBI.GRCh38'
'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  6.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.7Mb
Package suggested but not available for checking: 'gurobi'
Error(s) in re-building vignettes:
--- re-building 'MatchIt.Rmd' using rmarkdown
--- finished re-building 'MatchIt.Rmd'

--- re-building 'assessing-balance.Rmd' using rmarkdown

Quitting from lines 274-282 [unnamed-chunk-17] (assessing-balance.Rmd)
Error: processing vignette 'assessing-balance.Rmd' failed with diagnostics:
attempt to select less than one element in get1index
--- failed re-building 'assessing-balance.Rmd'

--- re-building 'estimating-effects.Rmd' using rmarkdown
--- finished re-building 'estimating-effects.Rmd'

--- re-building 'matching-methods.Rmd' using rmarkdown
--- finished re-building 'matching-methods.Rmd'

--- re-building 'sampling-weights.Rmd' using rmarkdown
--- finished re-building 'sampling-weights.Rmd'

SUMMARY: processing the following file failed:
  'assessing-balance.Rmd'

Error: Vignette re-building failed.
Execution halted
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
qr.X: no visible binding for global variable 'R'
Undefined global functions or variables:
  R
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
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
Package suggested but not available for checking: 'RGtk2'
'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
Package suggested but not available for checking: 'MethylCapSig'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
'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:
    extdata   3.4Mb
    libs      1.1Mb
'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: 'INLA'
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'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      2.1Mb
    help   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'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:
    data       3.0Mb
    examples  10.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.8Mb
    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
Package suggested but not available for checking: 'structSSI'
'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
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    lib    1.3Mb
    libs   1.2Mb
Found the following apparent S3 methods exported but not registered:
  plot.icss print.icss print.micss
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'midfielddata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'mixRasch'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'smooth.construct.unc_pcre.smooth.spec' not found
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    include   9.7Mb
    libs     17.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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   4.4Mb
'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
Package suggested but not available for checking: 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Packages suggested but not available for checking:
  'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 14.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   1.5Mb
'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.
'LazyData' is specified without 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  8.5Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    data   4.5Mb
    libs   1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
'LazyData' is specified without a 'data' directory
Found the following apparent S3 methods exported but not registered:
  plot.prevalence.msm plot.survfit.msm
See section 'Registering S3 methods' 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
Running examples in 'mtvc-Ex.R' failed
The error most likely occurred in:

> ### Name: mtvc
> ### Title: (mtvc) Multiple Time Varying Covariates
> ### Aliases: mtvc
> 
> ### ** Examples
> 
> data(simwide)
> cp.dataframe=mtvc(data=simwide,
+ origin='1970-01-01',
+ dates=c(FIRST_CHRONIC,FIRST_ACUTE,FIRST_RELAPSE),
+ complications=c(CHRONIC,ACUTE,RELAPSE),
+ start=DATETRAN,
+ stop=DLASTSE,
+ event=EVENT)
Error in `mutate()`:
ℹ In argument: `FIRST_CHRONIC = (structure(function (..., .x = ..1, .y =
  ..2, . = ..1) ...`.
Caused by error in `as.Date.numeric()`:
! 'origin' must be supplied
Backtrace:
     ▆
  1. ├─mtvc::mtvc(...)
  2. │ └─data %>% ungroup() %>% mutate(id = row_number()) %>% ...
  3. ├─dplyr::mutate_at(...)
  4. │ ├─dplyr::mutate(.tbl, !!!funs)
  5. │ └─dplyr:::mutate.data.frame(.tbl, !!!funs)
  6. │   └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  7. │     ├─base::withCallingHandlers(...)
  8. │     └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
  9. │       └─mask$eval_all_mutate(quo)
 10. │         └─dplyr (local) eval()
 11. ├─mtvc (local) `<inln_cl_>`(FIRST_CHRONIC)
 12. │ └─rlang::eval_bare(`_quo`, base::parent.frame())
 13. ├─rlang (local) as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 14. ├─base::as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 15. ├─base::as.Date.numeric(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 16. │ └─base::stop("'origin' must be supplied")
 17. └─base::.handleSimpleError(...)
 18.   └─dplyr (local) h(simpleError(msg, call))
 19.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
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
Found the following apparent S3 methods exported but not registered:
  plot.TetraDualStatis summary.TetraDualStatis
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   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
Package suggested but not available for checking: 'rTubeDB'
Package unavailable to check Rd xrefs: 'rTubeDB'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     2.4Mb
    models   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spatialClust'
'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
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    6.5Mb
    libs   1.2Mb
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
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
'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:

$fun.list$chromStart
function (x, ...)  .Primitive("as.integer")

$fun.list$chromEnd
function (x, ...)  .Primitive("as.integer")


$pattern
[1] "(chr.*?):([0-9]+)(?:-([0-9]+))?"

> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  8.96 0.55 9.5 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  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
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
Package suggested but not available for checking: 'fastshp'
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
GNU make is a SystemRequirements.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'NGCHMDemoData', 'NGCHMSupportFiles'
'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   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    CppCode   4.9Mb
    R         7.4Mb
    include  11.7Mb
    libs      1.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Package which this enhances but not available for checking: 'jpndistrict'
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  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
'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
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
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   2.6Mb
    mods   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
Found the following apparent S3 methods exported but not registered:
  print.fkk.test
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs   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
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            1.6Mb
    test_files   4.2Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.1Mb
    libs   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   1.1Mb
'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  6.8Mb
  sub-directories of 1Mb or more:
    doc   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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    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
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'unix'
GNU make is a SystemRequirements.
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs   19.6Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    data     1.5Mb
    libs     4.8Mb
    models   4.8Mb
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  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   1.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      1.4Mb
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
Package suggested but not available for checking: 'rrelaxiv'
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/orbweaver.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'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:
    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
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rcplex'
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 15.2Mb
  sub-directories of 1Mb or more:
    library  14.4Mb
Package which this enhances but not available for checking: 'CorShrink'
'LazyData' is specified without 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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.3Mb
'ctree.Rnw' using 'UTF-8'... [11s] NOTE
differences from 'ctree.Rout.save'
1409,1412d1408
< Deviance Residuals: 
<     Min       1Q   Median       3Q      Max  
< -45.801  -11.208   -1.049   10.903   53.615  
< 
  'partykit.Rnw'... [3s] OK
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
GNU make is a SystemRequirements.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    help   2.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    help   3.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    help   2.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    help   3.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    help   3.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lib    2.8Mb
    libs   2.3Mb
'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   2.7Mb
    doc    1.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   8.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'PythonInR'
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs    6.9Mb
    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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   2.2Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'DMwR'
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   1.2Mb
'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       1.5Mb
    extdata   3.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without 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: 'pinnacle.API'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(platetools)
  > 
  > test_check("platetools")
  [ FAIL 2 | WARN 1 | SKIP 4 | PASS 187 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • empty test (4): 'test-set_block.R:37:1', 'test-set_block.R:43:1',
    'test-set_block.R:48:1', 'test-set_block.R:53:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot_wrapper.R:33:5'): returns expected ggplot object ────────
  length(out96) not equal to 9L.
  1/1 mismatches
  [1] 11 - 9 == 2
  ── Failure ('test-plot_wrapper.R:34:5'): returns expected ggplot object ────────
  names(out96) not equal to c(...).
  Lengths differ: 11 is not 9
  
  [ FAIL 2 | WARN 1 | SKIP 4 | PASS 187 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tests   3.1Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'plot3logit-overview.Rmd' using rmarkdown

Quitting from lines 231-232 [unnamed-chunk-10] (plot3logit-overview.Rmd)
Error: processing vignette 'plot3logit-overview.Rmd' failed with diagnostics:
could not find function "guides_train"
--- failed re-building 'plot3logit-overview.Rmd'

SUMMARY: processing the following file failed:
  'plot3logit-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
'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:
    htmlwidgets   3.9Mb
'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
Package suggested but not available for checking: 'pmartRdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pollimetrydata'
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.8Mb
    libs   1.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      1.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data      2.7Mb
    extdata   3.5Mb
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
'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   5.0Mb
'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
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc  10.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata  11.6Mb
Package which this enhances but not available for checking: 'ffbase'
Unknown package 'ffbase' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    extdata   9.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinyApp   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.3Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    4.7Mb
    libs   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
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
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
Packages suggested but not available for checking: 'unix', 'cmdstanr'
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
    proj   7.7Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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'
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/prqlr.Rcheck/00install.out' for details.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is  9.5Mb
  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
'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:
    doc        4.0Mb
    examples   2.6Mb
Running examples in 'PTXQC-Ex.R' failed
The error most likely occurred in:

> ### Name: plot_RatiosPG
> ### Title: Plot ratios of labeled data (e.g. SILAC) from proteinGroups.txt
> ### Aliases: plot_RatiosPG
> 
> ### ** Examples
> 
> 
>  x1 = seq(-3, 3, by = 0.1)
>  y1 = dnorm(x1)
>  x2 = seq(-5, 1, by = 0.1)
>  y2 = dnorm(x2, mean = -1)
>  data = data.frame( x = c(x1,x2),
+                     y = c(y1,y2), 
+                     col = c(rep("ok", length(x1)), rep("shifted", length(x2))), 
+                     ltype = c(rep("solid", length(x1)), rep("dotted", length(x2))))
>  plot_RatiosPG(data, range(data$x), "Ratio plot", "red", "group")
Error in as.vector(x, "character") : 
  cannot coerce type 'environment' to vector of type 'character'
Calls: <Anonymous> ... validDetails.text -> as.character -> as.character.default
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   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
'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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 10.9Mb
  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.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      2.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.0Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    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:
    data   3.8Mb
    libs   1.4Mb
'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: 'fastshp'
'LazyData' is specified without 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         2.0Mb
    shiny_app   1.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'bootmlm'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   5.0Mb
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.
Package suggested but not available for checking: 'BRugs'
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    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
Error(s) in re-building vignettes:
--- re-building 'RAbHIT-vignette.Rmd' using rmarkdown

Quitting from lines 199-201 [unnamed-chunk-8] (RAbHIT-vignette.Rmd)
Error: processing vignette 'RAbHIT-vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'RAbHIT-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs          2.1Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 10.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets  10.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   6.8Mb
'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
Package suggested but not available for checking: 'gurobi'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
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: 'cairoDevice', 'RGtk2'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   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: 'raybevel'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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:
>     infile <- system.file("extdata", "hmp50.bz2", package = "rbiom")
>     biom <- read.biom(infile)
>     
>     sample.names(biom)
 [1] "HMP01" "HMP02" "HMP03" "HMP04" "HMP05" "HMP06" "HMP07" "HMP08" "HMP09"
[10] "HMP10" "HMP11" "HMP12" "HMP13" "HMP14" "HMP15" "HMP16" "HMP17" "HMP18"
[19] "HMP19" "HMP20" "HMP21" "HMP22" "HMP23" "HMP24" "HMP25" "HMP26" "HMP27"
[28] "HMP28" "HMP29" "HMP30" "HMP31" "HMP32" "HMP33" "HMP34" "HMP35" "HMP36"
[37] "HMP37" "HMP38" "HMP39" "HMP40" "HMP41" "HMP42" "HMP43" "HMP44" "HMP45"
[46] "HMP46" "HMP47" "HMP48" "HMP49" "HMP50"
> 
> 
> 
> 
> cleanEx()
> nameEx("select")
> ### * select
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: select
> ### Title: Reduce samples to a specific list
> ### Aliases: select
> 
> ### ** Examples
> 
>     library(rbiom)
>     
>     infile <- system.file("extdata", "hmp50.bz2", package = "rbiom")
>     biom <- read.biom(infile)
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
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
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    cont  24.2Mb
'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
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
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  7.8Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.5Mb
    po    2.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/Rcplex.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
    libs      1.2Mb
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    include  46.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.1Mb
GNU make is a SystemRequirements.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include        2.0Mb
    jsonexamples   3.8Mb
    libs           2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
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
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.5Mb
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
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'LazyData' is specified without a 'data' directory
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  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    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  7.9Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.3Mb
'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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/restfulr.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs      1.6Mb
    models    1.6Mb
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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    data  13.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warnings in file 'R/shinyFSSA.R':
  unable to translate 'f(<U+03C4>)' to native encoding
  unable to translate 'g(<U+03C4>)' to native encoding
  unable to translate 'f(<U+03C4>) + g(<U+03C4>)' to native encoding

Warnings in file 'R/shinyMFSSA.R':
  unable to translate 'A.1t(<U+03C9>1,<U+2113>) F1 +' to native encoding
  unable to translate 'A.2t(<U+03C9>2) F2' to native encoding
'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      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'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  9.2Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    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
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
'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'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  8.1Mb
  sub-directories of 1Mb or more:
    lib    3.4Mb
    libs   4.2Mb
File 'RInside/libs/x64/RInside.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/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_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.
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
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 x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.2/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  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'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:
    include   3.1Mb
    libs      2.4Mb
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 50.2Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  45.7Mb
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    extdata  23.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    hdf5     16.0Mb
    include   6.5Mb
    lib       2.6Mb
    libs      8.2Mb
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  7.0Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
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:
+ })
ERROR: Detected objects with duplicated names (A). Only the last occurance of each duplicated object will be available in MATLAB if completed: writeMat.default(filename, A = A, B = B, A = C) 
> 
> 
> ## Not run: 
> ##D # When writing to a stream connection the receiver needs to know on
> ##D # beforehand how many bytes are available. This can be done by using
> ##D # the 'onWrite' argument.
> ##D onWrite <- function(x)
> ##D   writeBin(x$length, con = x$con, size = 4, endian = "little")
> ##D   writeMat(con, A = A, B = B, onWrite = onWrite)
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  134.24 415.56 552.79 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  9.4Mb
  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
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs       1.0Mb
    minizinc   2.3Mb
'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'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
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 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.3Mb
'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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/RobLoxBioC.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              1.3Mb
    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
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'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:
    R         2.7Mb
    extdata   2.7Mb
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/ROracle.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   1.6Mb
Package suggested but not available for checking: 'RandomFields'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'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 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   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
installed size is  5.2Mb
  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 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
GNU make is a SystemRequirements.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.2/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/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.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/rsgeo.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/rshift.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without 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 19.3Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    4.7Mb
    libs  12.1Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lib    2.1Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs    1.1Mb
    swipl  37.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.4Mb
    help   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    rmarkdown  11.1Mb
GNU make is a SystemRequirements.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'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:
    R   5.0Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   9.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
'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
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:
> nameEx("writeBinFragments")
> ### * writeBinFragments
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: writeBinFragments
> ### Title: Writes binary data to disjoint sections of a connection or a
> ###   file
> ### Aliases: writeBinFragments.default writeBinFragments
> ### Keywords: IO
> 
> ### ** Examples
> ## Not run: # See example(readBinFragments.connection)
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  218.94 643.42 872.78 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 which this enhances but not available for checking: 'glmmADMB'
'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   5.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs      5.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rWCVPdata'
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  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.9Mb
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  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   2.6Mb
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  6.5Mb
  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
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  13.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   1.3Mb
Package suggested but not available for checking: 'networkTomography'
'sandwich-CL.Rnw'... [14s] NOTE
differences from 'sandwich-CL.Rout.save'
82c82
< Classes and Methods for R originally developed in the
---
> Classes and Methods for R developed in the
85,87c85,87
< Stanford University (2002-2015),
< by and under the direction of Simon Jackman.
< hurdle and zeroinfl functions by Achim Zeileis.
---
> Stanford University
> Simon Jackman
> hurdle and zeroinfl functions by Achim Zeileis
  'sandwich-OOP.Rnw'... [3s] OK
  'sandwich.Rnw'... [1s] OK
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(santaR)
  
  This is santaR version 1.2.3 
  
  > 
  > test_check("santaR")
  spar-finding: non-finite value inf; using BIG value
  [ FAIL 8 | WARN 2 | SKIP 0 | PASS 686 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_dfSearch-get_eigen_DFoverlay_list.R:30:3'): default values, change df ──
  length(result_DFoverlay[[1]]) not equal to 9.
  1/1 mismatches
  [1] 11 - 9 == 2
  ── Failure ('test_dfSearch-get_eigen_DFoverlay_list.R:45:3'): change nPC ───────
  length(result_DFoverlay[[1]]) not equal to 9.
  1/1 mismatches
  [1] 11 - 9 == 2
  ── Failure ('test_dfSearch-get_eigen_DFoverlay_list.R:61:3'): change step ──────
  length(result_DFoverlay[[1]]) not equal to 9.
  1/1 mismatches
  [1] 11 - 9 == 2
  ── Failure ('test_dfSearch-get_eigen_DFoverlay_list.R:77:3'): no showPt ────────
  length(result_DFoverlay[[1]]) not equal to 9.
  1/1 mismatches
  [1] 11 - 9 == 2
  ── Failure ('test_dfSearch-get_eigen_DFoverlay_list.R:92:3'): no autofit ───────
  length(result_DFoverlay[[1]]) not equal to 9.
  1/1 mismatches
  [1] 11 - 9 == 2
  ── Failure ('test_dfSearch-plot_nbTP_histogram.R:37:3'): default values ────────
  length(result_nbTPHisto) not equal to 9.
  1/1 mismatches
  [1] 11 - 9 == 2
  ── Failure ('test_dfSearch-plot_nbTP_histogram.R:51:3'): different number of time-points per spline ──
  length(result_nbTPHisto_2) not equal to 9.
  1/1 mismatches
  [1] 11 - 9 == 2
  ── Failure ('test_dfSearch-plot_nbTP_histogram.R:69:3'): change dfCuttOff ──────
  length(result_nbTPHisto) not equal to 9.
  1/1 mismatches
  [1] 11 - 9 == 2
  
  [ FAIL 8 | WARN 2 | SKIP 0 | PASS 686 ]
  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
Package suggested but not available for checking: 'FitARMA'
Running examples in 'saros-Ex.R' failed
The error most likely occurred in:

> ### Name: embed_cat_prop_plot
> ### Title: Embed Interactive Categorical Plot
> ### Aliases: embed_cat_prop_plot
> 
> ### ** Examples
> 
> embed_cat_prop_plot(data = ex_survey, dep = b_1:b_3)
Error in `setup_elements()`:
! Can't merge the `text` theme element.
Caused by error in `merge_element()`:
! Only elements of the same class can be merged.
Backtrace:
     ▆
  1. ├─base (local) `<fn>`(x)
  2. └─ggplot2:::print.ggplot(x)
  3.   ├─ggplot2::ggplot_gtable(data)
  4.   └─ggplot2:::ggplot_gtable.ggplot_built(data)
  5.     └─plot$guides$assemble(theme)
  6.       └─ggplot2 (local) assemble(..., self = self)
  7.         └─self$draw(theme, default_position, theme$legend.direction)
  8.           └─ggplot2 (local) draw(..., self = self)
  9.             └─guides[[i]]$draw(...)
 10.               └─ggplot2 (local) draw(..., self = self)
 11.                 └─self$setup_elements(params, self$elements, theme)
 12.                   └─ggplot2 (local) setup_elements(...)
 13.                     ├─ggplot2::calc_element("legend.title", add_theme(theme, title))
 14.                     └─ggplot2:::add_theme(theme, title)
 15.                       ├─rlang::try_fetch(...)
 16.                       │ ├─base::tryCatch(...)
 17.                       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 18.                       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 19.                       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 20.                       │ └─base::withCallingHandlers(...)
 21.                       ├─ggplot2::merge_element(t2[[item]], t1[[item]])
 22.                       └─ggplot2:::merge_element.element(t2[[item]], t1[[item]])
 23.                         └─cli::cli_abort("Only elements of the same class can be merged.")
 24.                           └─rlang::abort(...)
Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(saros)
  > 
  > testthat::test_check("saros")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 184 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-draft_report.R:4:3'): draft_report ─────────────────────────────
  Error in `setup_elements(...)`: Can't merge the `text` theme element.
  Caused by error in `merge_element()`:
  ! Only elements of the same class can be merged.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 184 ]
  Error: Test failures
  Execution halted
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   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  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
'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.
Warning in file 'R/label-number.R':
  unable to translate '<U+03BC>s' to native encoding
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  'sceasy', 'SeuratDisk', 'SeuratWrappers'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
'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:
    R   8.1Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
'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      1.5Mb
    libs   2.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following apparent S3 methods exported but not registered:
  model.matrix.segmented model.matrix.stepmented vcov.stepmented
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
'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
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    www  34.4Mb
'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  5.0Mb
  sub-directories of 1Mb or more:
    libs     3.3Mb
    models   1.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
'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
Package suggested but not available for checking: 'BPCells'
Packages suggested but not available for checking: 'BPCells', 'presto'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   4.9Mb
'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   5.1Mb
installed size is 78.5Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    gdal     2.8Mb
    libs    61.7Mb
    proj     7.7Mb
    sqlite   1.5Mb
Found the following significant warnings:

  Warning: 'lwgeom::st_perimeter' is deprecated.
  Warning: 'lwgeom::st_perimeter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
'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  6.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rCOSA'
Package unavailable to check Rd xrefs: 'rCOSA'
Package suggested but not available for checking: 'hydromad'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/shide.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.4Mb
'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
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   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
'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
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    www   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
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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    help      1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      1.5Mb
'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.
'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: 'INLA'
'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      2.2Mb
    libs   1.5Mb
'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
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  5.5Mb
  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   4.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   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
Package suggested but not available for checking: 'gurobi'
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 Title field: should not end in a period.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/smcryptoR.Rcheck/00install.out' for details.
Running examples in 'SMDIC-Ex.R' failed
The error most likely occurred in:

> ### Name: exp2cell
> ### Title: exp2cell
> ### Aliases: exp2cell
> 
> ### ** Examples
> 
> #get breast cancer gene expression profile.
> exp.example<-GetExampleData("exp.example")
> 
> #perform the exp2cell method. Method must be one of "xCell","ssGSEA" and "CIBERSORT".
> cellmatrix<-exp2cell(exp=exp.example,method="ssGSEA") #cell abundance matrix
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SMDIC.Rmd' using rmarkdown

Quitting from lines 63-70 [unnamed-chunk-2] (SMDIC.Rmd)
Error: processing vignette 'SMDIC.Rmd' failed with diagnostics:
useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
--- failed re-building 'SMDIC.Rmd'

SUMMARY: processing the following file failed:
  'SMDIC.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  6.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
'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  6.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.3Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
Warnings in file 'R/replace_special_characters_internal.R':
  unable to translate '<U+00C4>' to native encoding
  unable to translate '<U+00D6>' to native encoding
  unable to translate '<U+00DC>' to native encoding
  unable to translate '<U+00E4>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00FC>' to native encoding
  unable to translate '<U+00DF>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
'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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     3.3Mb
    doc   1.1Mb
'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   1.3Mb
    doc    1.3Mb
    libs   1.7Mb
'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  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NLMR'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R   4.6Mb
Package suggested but not available for checking: 'NLMR'
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    libs   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  6.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    java   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package 'sparsebn' in Rd xrefs
'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 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.0Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', '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.explore', 'spatstat.model',
  '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.explore', 'spatstat.model', '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.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
'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  8.1Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
    etc   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
'LazyData' is specified without a 'data' directory
Warnings in file 'R/import_csv_settings.R':
  unable to translate '(W/m<U+00B2>*nm)' to native encoding
  unable to translate '(mW/m<U+00B2>*nm)' to native encoding
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    doc       1.1Mb
    extdata   2.6Mb
    libs      1.6Mb
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spork)
  > 
  > test_check("spork")
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 101 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-spork.R:451:3', 'test-spork.R:469:3',
    'test-spork.R:490:3', 'test-spork.R:540:3', 'test-spork.R:567:3',
    'test-spork.R:615:3', 'test-spork.R:623:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-spork.R:297:1'): spork to plotmath is stable ───────────────────
  Error in `as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)`: cannot coerce class '"plotmath"' to a data.frame
  Backtrace:
       ▆
    1. ├─... %>% as_preview() at test-spork.R:297:1
    2. ├─spork::as_preview(.)
    3. └─spork:::as_preview.plotmath(.)
    4.   ├─latexpdf::as.png(...)
    5.   └─spork:::as.png.plotmath(...)
    6.     ├─ggplot2::ggplot(x, ...)
    7.     └─spork:::ggplot.plotmath(x, ...)
    8.       ├─ggplot2::ggplot(data.frame(x = 1, y = 1, label = (x)))
    9.       └─base::data.frame(x = 1, y = 1, label = (x))
   10.         ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
   11.         └─base::as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 101 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'BalancedSampling::lcubeflightphase'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'spq_userguide.Rmd' using rmarkdown

Quitting from lines 500-501 [unnamed-chunk-24] (spq_userguide.Rmd)
Error: processing vignette 'spq_userguide.Rmd' failed with diagnostics:
Invalid index: field name 'x_start' not found
--- failed re-building 'spq_userguide.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.2Mb
'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
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    shiny-squid   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 16.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  13.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.9Mb
  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
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    include  11.3Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
GNU make is a SystemRequirements.
'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  6.3Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    1.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.4Mb
Package suggested but not available for checking: 'asreml'
Running 'testthat.R' [63s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(statgenGxE)
  > 
  > test_check("statgenGxE")
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 448 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • On CRAN (17): 'test-gxeMegaEnv.R:72:3', 'test-gxeMegaEnv.R:103:3',
    'test-gxeVarComp.R:52:3', 'test-gxeVarComp.R:116:3',
    'test-gxeVarComp.R:151:3', 'test-gxeVarComp.R:187:3',
    'test-gxeVarComp.R:216:3', 'test-gxeVarCov.R:24:3', 'test-gxeVarCov.R:37:3',
    'test-gxeVarCov.R:78:3', 'test-gxeVarCov.R:90:3', 'test-gxeVarCov.R:100:3',
    'test-report.R:7:3', 'test-report.R:21:3', 'test-report.R:31:3',
    'test-report.R:41:3', 'test-summaries.R:75:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plots.R:440:3'): option colorGenoBy in megaEnv plot functions correctly ──
  setdiff(layout[["name"]], layout0[["name"]]) not equal to "guide-box".
  Lengths differ: 0 is not 1
  
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 448 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'asreml'
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))
Package suggested but not available for checking: 'networksis'
'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
Package suggested but not available for checking: 'INLA'
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
'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  6.8Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/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
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   1.1Mb
'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
Missing or unexported objects:
  'GSVA::gsvaParam' 'GSVA::ssgseaParam'
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown

Quitting from lines 139-147 [unnamed-chunk-5] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
'gsvaParam' is not an exported object from 'namespace:GSVA'
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'extraTrees'
'LazyData' is specified without a 'data' directory
surfaceSimulate : phytransform: no visible global function definition
  for 'rescale'
Undefined global functions or variables:
  rescale
'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: 'INLA'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.2Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
Package suggested but not available for checking: 'distr6'
Unknown package 'distr6' in Rd xrefs
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.9Mb
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   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
Package suggested but not available for checking: 'swephRdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'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   2.9Mb
    doc    1.8Mb
'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  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.4Mb
'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
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
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc  12.3Mb
Error(s) in re-building vignettes:
--- re-building 'tciu-LT-kimesurface.Rmd' using rmarkdown

Quitting from lines 159-160 [unnamed-chunk-5] (tciu-LT-kimesurface.Rmd)
Error: processing vignette 'tciu-LT-kimesurface.Rmd' failed with diagnostics:
Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `scales_add_defaults()`:
! could not find function "scales_add_defaults"
--- failed re-building 'tciu-LT-kimesurface.Rmd'

--- re-building 'tciu-fMRI-analytics.Rmd' using rmarkdown
--- finished re-building 'tciu-fMRI-analytics.Rmd'

SUMMARY: processing the following file failed:
  'tciu-LT-kimesurface.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    8.0Mb
    libs   1.1Mb
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
Package suggested but not available for checking: 'INLA'
'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   5.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    4.5Mb
    help   2.7Mb
'LazyData' is specified without a 'data' directory
installed size is 78.7Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    gdal   2.8Mb
    libs  64.6Mb
    proj   7.7Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       7.2Mb
    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
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
'LazyData' is specified without a 'data' directory
Unknown package 'textreadr' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
'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
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: declared S3 method 'filter.edsurvey.data.frame' not found
See section 'Generic functions and methods' 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
Warning: declared S3 method 'filter.Seurat' not found
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   4.5Mb
Package suggested but not available for checking: 'rrelaxiv'
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.0Mb
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
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    examples  12.7Mb
    include    3.6Mb
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'
Running 'testthat.R' [37s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tmt)
  - tmt 0.3.1-2 (2022-05-16)
  > 
  > test_check("tmt")
  The following items are specified in the dataset, but not in the submitted mstdesign: ii1 
  The following items are specified in the mstdesign, but not in the dataset: i1 
  The following items are specified in the dataset, but not in the submitted mstdesign: i1 
  The following items are specified in the mstdesign, but not in the dataset: ii1 
  The following items are specified in the dataset, but not in the submitted mstdesign: ii1 
  The following items are specified in the mstdesign, but not in the dataset: i1 
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 346 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-tmt_gmc.R:34:5'): tmt_gmc data structure ─────────────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 11 - 9 == 2
  Backtrace:
      ▆
   1. └─testthat::expect_that(length(p), equals(9)) at test-tmt_gmc.R:34:5
   2.   └─testthat (local) condition(object)
   3.     └─testthat::expect_equal(x, expected, ..., expected.label = label)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 346 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/tok.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data-tables   1.4Mb
    doc           1.9Mb
    help          1.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RGtk2'
Package suggested but not available for checking: 'gurobi'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/topologyGSA.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    R         5.6Mb
    help      1.6Mb
    include   1.8Mb
    libs     17.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'toscaData'
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taxidata'
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  13.3Mb
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'fwelnet', 'doMC'
'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:
  'Eunomia', 'CohortGenerator', 'CirceR', 'Capr'
Package suggested but not available for checking: 'TreeDistData'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    doc       1.3Mb
    extdata  14.8Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'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
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'transform.bal_oversampling' not found
Warning: declared S3 method 'transform.bal_subsampling' not found
Warning: declared S3 method 'transform.cla_fs' not found
Warning: declared S3 method 'transform.ts_aug_awareness' not found
Warning: declared S3 method 'transform.ts_aug_awaresmooth' not found
Warning: declared S3 method 'transform.ts_aug_flip' not found
Warning: declared S3 method 'transform.ts_aug_jitter' not found
Warning: declared S3 method 'transform.ts_aug_none' not found
Warning: declared S3 method 'transform.ts_aug_shrink' not found
Warning: declared S3 method 'transform.ts_aug_stretch' not found
Warning: declared S3 method 'transform.ts_aug_wormhole' not found
Warning: declared S3 method 'transform.ts_fil_ema' not found
Warning: declared S3 method 'transform.ts_fil_hp' not found
Warning: declared S3 method 'transform.ts_fil_kalman' not found
Warning: declared S3 method 'transform.ts_fil_lowess' not found
Warning: declared S3 method 'transform.ts_fil_ma' not found
Warning: declared S3 method 'transform.ts_fil_none' not found
Warning: declared S3 method 'transform.ts_fil_qes' not found
Warning: declared S3 method 'transform.ts_fil_recursive' not found
Warning: declared S3 method 'transform.ts_fil_seas_adj' not found
Warning: declared S3 method 'transform.ts_fil_ses' not found
Warning: declared S3 method 'transform.ts_fil_smooth' not found
Warning: declared S3 method 'transform.ts_fil_spline' not found
Warning: declared S3 method 'transform.ts_fil_winsor' not found
Warning: declared S3 method 'transform.ts_norm_none' not found
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    ubinc   2.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.0Mb
    libs   4.4Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.5Mb
Running examples in 'ufs-Ex.R' failed
The error most likely occurred in:

> ### Name: duoComparisonDiamondPlot
> ### Title: meansComparisonDiamondPlot and duoComparisonDiamondPlot
> ### Aliases: duoComparisonDiamondPlot meansComparisonDiamondPlot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 
> meansComparisonDiamondPlot(mtcars,
+                            items=c('disp', 'hp'),
+                            compareBy='vs',
+                            xbreaks=c(100,200, 300, 400));
> meansComparisonDiamondPlot(chickwts,
+                            items='weight',
+                            compareBy='feed',
+                            xbreaks=c(100,200,300,400),
+                            showData=FALSE);
> duoComparisonDiamondPlot(mtcars,
+                          items=c('disp', 'hp'),
+                          compareBy='vs',
+                          xbreaks=c(100,200, 300, 400));
Error: Cannot create zero-length unit vector ("unit" subsetting)
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  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
'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/4.2/unigd.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 18.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.4Mb
    libs  14.7Mb
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
Package suggested but not available for checking: 'USA.state.boundaries.data'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  15.3Mb
Package required and available but unsuitable version: 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'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
installed size is 74.9Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    gdal      2.8Mb
    libs     60.3Mb
    proj      7.7Mb
'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
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      8.5Mb
GNU make is a SystemRequirements.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
'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  7.8Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    help   3.0Mb
Missing link or links in documentation object 'profilevglm.Rd':
  '[stats]{plot.profile}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
'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:
    doc    2.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
Running examples in 'visR-Ex.R' failed
The error most likely occurred in:

> ### Name: add_highlight
> ### Title: Highlight a specific strata
> ### Aliases: add_highlight add_highlight.ggsurvfit
> 
> ### ** Examples
> 
> 
> adtte %>%
+   visR::estimate_KM(strata = "SEX") %>%
+   visR::visr() %>%
+   visR::add_CI(alpha = 0.4) %>%
+   visR::add_highlight(strata = "M", bg_alpha = 0.2)
Error in FUN(X[[i]], ...) : 
  The strata you specified has not been found in the provided plot.
  Available strata: NULL, NULL
  Please adjust and rerun.
Calls: %>% ... add_highlight.ggsurvfit -> <Anonymous> -> lapply -> FUN
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning: 'ggiraph' is deprecated.
  Warning: 'ggiraph' is deprecated.
  Warning: 'ggiraph' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/vol2birdR.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  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'changing_default_parameters.Rmd' using rmarkdown
--- finished re-building 'changing_default_parameters.Rmd'

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

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

Quitting from lines 68-71 [unnamed-chunk-2] (process_bouts.Rmd)
Error: processing vignette 'process_bouts.Rmd' failed with diagnostics:
'origin' must be supplied
--- failed re-building 'process_bouts.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   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
Package suggested but not available for checking: 'prepr'
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'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   4.8Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 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.
'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 12.7Mb
  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  7.0Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    help   1.9Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
Found the following problems:
retrieveFunctionReturnTypes.Rd:48:38: Warning: nested emphasis <code>


retrieveFunctionReturnTypes.Rd:52:38: Warning: nested emphasis <code>


retrieveFunctionReturnTypes.Rd:56:38: Warning: nested emphasis <code>


retrieveTestCaseDefinitions.Rd:52:38: Warning: nested emphasis <code>


retrieveTestCaseDefinitions.Rd:56:38: Warning: nested emphasis <code>


retrieveTestCaseDefinitions.Rd:61:38: Warning: nested emphasis <code>
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/x13binary.Rcheck/00install.out' for details.
'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   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    java  25.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/xLLiM.Rcheck/00install.out' for details.
'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  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    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
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/ymd.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/zoomerjoin.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory