installed size is  8.9Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 31-79 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'org.Hs.eg.db', 'clusterProfiler'
Packages required but not available: 'GenomicRanges', 'rtracklayer'

Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
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--- re-building ‘CPMandPERT.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Quitting from lines 147-148 (CPMandPERT.Rmd) 
Error: processing vignette 'CPMandPERT.Rmd' failed with diagnostics:
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--- re-building ‘LESS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘pcaMethods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Crossover.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
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--- re-building ‘using-crossva-and-openva.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error(s) in re-building vignettes:
--- re-building ‘plotting.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'crunch'

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

    filter, rstandard, setNames

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

    title

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    write.csv

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    table

Loading required package: dplyr

Attaching package: 'dplyr'

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

    combine, filter, id

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'ggplot2'

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

    resolution

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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 38.0Mb
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    libs  36.3Mb
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Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [85s/102s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  • TODO modify variablesFilter to distinguish between a fully specified variable subset and the original dataset (1)
  • TODO: distinguish this kind of attempted value updating from metadata updates (2)
  • TODO: ensure something about the elements of a 'list column' (1)
  • TODO: something intelligent with parentheses and order of operations (GH issue #99) (1)
  • empty test (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── [1m[38;5;214mFailure[39m (test-automation.R:92:9): Scripts catalog print method[22m ───────────────────────────
  formatScriptCatalog(...) not identical to data.frame(...).
  Component "Timestamp": 1 string mismatch
  
  [ [38;5;214mFAIL[39m 1 | [35mWARN[39m 7 | [34mSKIP[39m 15 | [32mPASS[39m 3502 ]
  Error: Test failures
  Total teardown: Time difference of 1.40667e-05 secs
  Execution halted
Packages required but not available: 'rJPSGCS', 'chopsticks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘cspp-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Please cite:

Caleb Lucas and Joshua McCrain (2020). cspp: A Package for The Correlates of State Policy Project Data.
R package version 0.3.1.

Jordan, Marty P. and Matt Grossmann. 2020. The Correlates of State Policy Project v.2.2.
East Lansing, MI: Institute for Public Policy and Social Research (IPPSR).

You are using version 2.2 of the CSPP data.

Quitting from lines 210-218 (cspp-vignette.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 180.5Mb
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    data    1.7Mb
    libs  175.6Mb
Package which this enhances but not available for checking: ‘pbdMPI’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/CUFF.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘cuperdec-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
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Error(s) in re-building vignettes:
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--- re-building ‘cutpointr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-52 (cutpointr.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_cvCovEst.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘RGtk2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: MASS
Loading required package: limSolve

Attaching package: 'ggplot2'

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

    resolution

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Error: processing vignette 'vignette.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Scoring_Rules_GEE.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 67-71 (Scoring_Rules_GEE.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
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    libs   5.2Mb
installed size is 10.1Mb
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    R      3.1Mb
    help   1.0Mb
    libs   5.6Mb
installed size is 28.7Mb
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Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("Cyclops")
  Loading required package: Cyclops
  Sorting outcomes by stratumId and rowId
  Sorting covariates by covariateId, stratumId, and rowId
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/CytobankAPIstats.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘cytofan_flow_cytometry.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 78-84 (cytofan_flow_cytometry.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 54-71 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/D2MCS.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-dabestr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 99-100 (using-dabestr.Rmd) 
Error: processing vignette 'using-dabestr.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Error(s) in re-building vignettes:
  ...
--- re-building ‘dagitty4semusers.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 33-48 (dagitty4semusers.Rmd) 
Error: processing vignette 'dagitty4semusers.Rmd' failed with diagnostics:
need finite 'ylim' values
--- failed re-building ‘dagitty4semusers.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dams.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: dams
Loading required package: ggplot2
Loading required package: maps
Loading required package: mapproj
Quitting from lines 70-71 (dams.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dann.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 30-51 (dann.Rmd) 
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--- re-building ‘sub_dann.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 100-103 (sub_dann.Rmd) 
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SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_danstat.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 113-125 (Introduction_to_danstat.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘SNPRelate’

Package suggested but not available for checking: ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/DatabaseConnectorJars.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/DatabaseConnector.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   4.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/DataClean.Rcheck/00install.out’ for details.
Packages required but not available: 'RGtk2', 'gWidgets2RGtk2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/DataLoader.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘extending_dataMaid.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Error: processing vignette 'extending_dataMaid.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignettes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-27 (vignettes.Rmd) 
Error: processing vignette 'vignettes.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘extending_dataReporter.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Datasaurus.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 47-55 (Datasaurus.Rmd) 
Error: processing vignette 'Datasaurus.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 68.4Mb
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    libs  67.4Mb
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    doc    1.7Mb
    libs   2.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘DataVisualizations.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 40-43 (DataVisualizations.Rmd) 
Error: processing vignette 'DataVisualizations.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Error(s) in re-building vignettes:
  ...
--- re-building ‘daymetr-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Sitename set to default - tmp
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   8.0Mb
Package required but not available: ‘RedeR’

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

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

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

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

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

Package suggested but not available for checking: ‘BRugs’

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

Package suggested but not available for checking: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘dcortools/libs/dcortools.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
    Objects: ‘RcppExports.o’, ‘matrix_vector_operations.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 62.7Mb
  sub-directories of 1Mb or more:
    libs  62.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error(s) in re-building vignettes:
--- re-building ‘algorithm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘algorithm.Rmd’

--- re-building ‘extend.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 205-213 (extend.Rmd) 
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--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'ddpcr'

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

    step

Reading data files into plate... DONE (1 seconds)
Initializing plate of type `custom_thresholds`... DONE (0 seconds)
Identifying outlier droplets... DONE (0 seconds)
Classifying droplets... DONE (0 seconds)
Analysis complete
Quitting from lines 133-151 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
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--- re-building ‘technical_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘technical_details.Rmd’

SUMMARY: processing the following files failed:
  ‘extend.Rmd’ ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘WGCNA’
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘example_decision_function.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 235-240 (example_decision_function.Rmd) 
Error: processing vignette 'example_decision_function.Rmd' failed with diagnostics:
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--- failed re-building ‘example_decision_function.Rmd’

--- re-building ‘wildfire_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘wildfire_example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19'

Package suggested but not available for checking: ‘VariantAnnotation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/DecorateR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/DeducerPlugInExample.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/DeducerPlugInScaling.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Deducer.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/DeducerSpatial.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/DeducerSurvival.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/DeducerText.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ODE_parameter_inference.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 115-125 (ODE_parameter_inference.Rmd) 
Error: processing vignette 'ODE_parameter_inference.Rmd' failed with diagnostics:
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--- failed re-building ‘ODE_parameter_inference.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/deisotoper.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘delayed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 97-98 (delayed.Rmd) 
Error: processing vignette 'delayed.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘delayed.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 104.0Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
  ...
--- re-building ‘dematel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 93-94 (dematel.Rmd) 
Error: processing vignette 'dematel.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘dematel.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘WGCNA’
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  39.1Mb
Error(s) in re-building vignettes:
--- re-building ‘derivmkts-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning in sprintf("%s$", extension, ignore.case = TRUE) :
  one argument not used by format '%s$'
Warning in sprintf("%s$", extension, ignore.case = TRUE) :
  one argument not used by format '%s$'
Quitting from lines 248-253 (derivmkts-vignette.Rmd) 
Error: processing vignette 'derivmkts-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘derivmkts-vignette.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘categorical-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 57-59 (categorical-data.Rmd) 
Error: processing vignette 'categorical-data.Rmd' failed with diagnostics:
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--- failed re-building ‘categorical-data.Rmd’

--- re-building ‘continuous-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 84-86 (continuous-data.Rmd) 
Error: processing vignette 'continuous-data.Rmd' failed with diagnostics:
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--- failed re-building ‘continuous-data.Rmd’

--- re-building ‘visualization.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 46-47 (visualization.Rmd) 
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘visualization.Rmd’

SUMMARY: processing the following files failed:
  ‘categorical-data.Rmd’ ‘continuous-data.Rmd’ ‘visualization.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.8Mb
    help   1.5Mb
    libs   3.8Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rsymphony'
Error(s) in re-building vignettes:
  ...
--- re-building ‘desplot_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 30-39 (desplot_examples.Rmd) 
Error: processing vignette 'desplot_examples.Rmd' failed with diagnostics:
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--- failed re-building ‘desplot_examples.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'dclone', 'dcmle'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘batch-mode.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘batch-mode.Rmd’

--- re-building ‘linescan-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘linescan-data.Rmd’

--- re-building ‘single-images.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-78 (single-images.Rmd) 
Error: processing vignette 'single-images.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘single-images.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-dfoliatR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 103-104 (intro-to-dfoliatR.Rmd) 
Error: processing vignette 'intro-to-dfoliatR.Rmd' failed with diagnostics:
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--- failed re-building ‘intro-to-dfoliatR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    libs  66.6Mb
Packages required but not available: 'MLInterfaces', 'genefilter', 'ALL'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DGEobj', 'edgeR', 'IHW', 'qvalue', 'RNASeqPower', 'sva', 'zFPKM'

Package suggested but not available for checking: ‘biomaRt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.7Mb
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.2Mb
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dialrjars)
  > 
  > test_check("dialrjars")
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/dialr.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 168-169 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘did-basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 129-131 (did-basics.Rmd) 
Error: processing vignette 'did-basics.Rmd' failed with diagnostics:
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--- failed re-building ‘did-basics.Rmd’

--- re-building ‘extensions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 97-119 (extensions.Rmd) 
Error: processing vignette 'extensions.Rmd' failed with diagnostics:
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--- failed re-building ‘extensions.Rmd’

--- re-building ‘multi-period-did.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘multi-period-did.Rmd’

--- re-building ‘pre-testing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 94-150 (pre-testing.Rmd) 
Error: processing vignette 'pre-testing.Rmd' failed with diagnostics:
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--- failed re-building ‘pre-testing.Rmd’

SUMMARY: processing the following files failed:
  ‘did-basics.Rmd’ ‘extensions.Rmd’ ‘pre-testing.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs   1.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.2Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Package suggested but not available for checking: ‘pcaL1’
Error(s) in re-building vignettes:
  ...
--- re-building ‘dint.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 254-287 (dint.Rmd) 
Error: processing vignette 'dint.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘dint.Rmd’

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

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

Package suggested but not available for checking: ‘edgeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘DirectEffects.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 150-165 (DirectEffects.Rmd) 
Error: processing vignette 'DirectEffects.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘DirectEffects.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using knitr
Quitting from lines 16-76 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘disaggregation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 106-107 (disaggregation.Rmd) 
Error: processing vignette 'disaggregation.Rmd' failed with diagnostics:
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--- failed re-building ‘disaggregation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'SingleCellExperiment', 'TSCAN', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 77-78 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

--- re-building ‘mixtures.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘mixtures.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic_usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 292-311 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
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--- failed re-building ‘basic_usage.Rmd’

--- re-building ‘market_clearing_assessment.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘market_clearing_assessment.Rmd’

--- re-building ‘package.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_disto.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 42-72 (vignette_disto.Rmd) 
Error: processing vignette 'vignette_disto.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vignette_disto.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    help   1.3Mb
    libs   3.0Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/DiversityOccupancy.Rcheck/00install.out’ for details.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
sh: line 1: 71416 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Bold Italic.ttf' '/Volumes/Temp/tmp/RtmplbJ1lh/fonts/Arial Narrow Bold Italic' 2>&1
sh: line 1: 71418 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Bold.ttf' '/Volumes/Temp/tmp/RtmplbJ1lh/fonts/Arial Narrow Bold' 2>&1
sh: line 1: 71420 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Italic.ttf' '/Volumes/Temp/tmp/RtmplbJ1lh/fonts/Arial Narrow Italic' 2>&1
sh: line 1: 71422 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow.ttf' '/Volumes/Temp/tmp/RtmplbJ1lh/fonts/Arial Narrow' 2>&1
sh: line 1: 71518 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Bold Italic.ttf' '/Volumes/Temp/tmp/RtmpDeRpJe/fonts/Arial Narrow Bold Italic' 2>&1
sh: line 1: 71521 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Bold.ttf' '/Volumes/Temp/tmp/RtmpDeRpJe/fonts/Arial Narrow Bold' 2>&1
sh: line 1: 71523 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Italic.ttf' '/Volumes/Temp/tmp/RtmpDeRpJe/fonts/Arial Narrow Italic' 2>&1
sh: line 1: 71526 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow.ttf' '/Volumes/Temp/tmp/RtmpDeRpJe/fonts/Arial Narrow' 2>&1
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: line 1: 71888 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Bold Italic.ttf' '/Volumes/Temp/tmp/RtmpTu16sQ/fonts/Arial Narrow Bold Italic' 2>&1
sh: line 1: 71892 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Bold.ttf' '/Volumes/Temp/tmp/RtmpTu16sQ/fonts/Arial Narrow Bold' 2>&1
sh: line 1: 71896 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Italic.ttf' '/Volumes/Temp/tmp/RtmpTu16sQ/fonts/Arial Narrow Italic' 2>&1
sh: line 1: 71902 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow.ttf' '/Volumes/Temp/tmp/RtmpTu16sQ/fonts/Arial Narrow' 2>&1
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: line 1: 72107 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Bold Italic.ttf' '/Volumes/Temp/tmp/RtmphsLTdh/fonts/Arial Narrow Bold Italic' 2>&1
sh: line 1: 72111 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Bold.ttf' '/Volumes/Temp/tmp/RtmphsLTdh/fonts/Arial Narrow Bold' 2>&1
sh: line 1: 72115 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Italic.ttf' '/Volumes/Temp/tmp/RtmphsLTdh/fonts/Arial Narrow Italic' 2>&1
sh: line 1: 72119 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow.ttf' '/Volumes/Temp/tmp/RtmphsLTdh/fonts/Arial Narrow' 2>&1
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: line 1: 72685 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Bold Italic.ttf' '/Volumes/Temp/tmp/RtmpqmBDdZ/fonts/Arial Narrow Bold Italic' 2>&1
sh: line 1: 72687 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Bold.ttf' '/Volumes/Temp/tmp/RtmpqmBDdZ/fonts/Arial Narrow Bold' 2>&1
sh: line 1: 72689 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Italic.ttf' '/Volumes/Temp/tmp/RtmpqmBDdZ/fonts/Arial Narrow Italic' 2>&1
sh: line 1: 72691 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow.ttf' '/Volumes/Temp/tmp/RtmpqmBDdZ/fonts/Arial Narrow' 2>&1
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: line 1: 73065 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Bold Italic.ttf' '/Volumes/Temp/tmp/Rtmp3WMauI/fonts/Arial Narrow Bold Italic' 2>&1
sh: line 1: 73067 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Bold.ttf' '/Volumes/Temp/tmp/Rtmp3WMauI/fonts/Arial Narrow Bold' 2>&1
sh: line 1: 73070 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow Italic.ttf' '/Volumes/Temp/tmp/Rtmp3WMauI/fonts/Arial Narrow Italic' 2>&1
sh: line 1: 73074 Segmentation fault: 11  '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/System/Library/Fonts/Supplemental/Arial Narrow.ttf' '/Volumes/Temp/tmp/Rtmp3WMauI/fonts/Arial Narrow' 2>&1
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘dlstats.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 48-58 (dlstats.Rmd) 
Error: processing vignette 'dlstats.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘dlstats.Rmd’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘dobin.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 190-200 (dobin.Rmd) 
Error: processing vignette 'dobin.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘dobin.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘geepack’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.8Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  13.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘da-logistic-regression.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 177-178 (da-logistic-regression.Rmd) 
Error: processing vignette 'da-logistic-regression.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘da-logistic-regression.Rmd’

SUMMARY: processing the following file failed:
  ‘da-logistic-regression.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'doMPI', 'doRedis'
Package unavailable to check Rd xrefs: ‘doMPI’
Error(s) in re-building vignettes:
  ...
--- re-building ‘button_types.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘button_types.Rmd’

--- re-building ‘customization.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘customization.Rmd’

--- re-building ‘downloadthis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 159-165 (downloadthis.Rmd) 
Error: processing vignette 'downloadthis.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘downloadthis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'alakazam', 'ggtree', 'shazam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘walk_through_in_R.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 33-38 (walk_through_in_R.Rmd) 
Error: processing vignette 'walk_through_in_R.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘walk_through_in_R.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/drawsample.Rcheck/00install.out’ for details.
Package required but not available: ‘qusage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GenomicRanges', 'GenomicFeatures',
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'org.Hs.eg.db'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘userGuide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 159-163 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘userGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dsa-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 122-146 (dsa-vignette.Rmd) 
Error: processing vignette 'dsa-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘dsa-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘start.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 88-102 (start.Rmd) 
Error: processing vignette 'start.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘start.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Designing-33PC.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 46-59 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Designing-33PC.Rmd’

SUMMARY: processing the following file failed:
  ‘Designing-33PC.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.3Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.5Mb
Error(s) in re-building vignettes:
--- re-building ‘parallelization-considerations.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘parallelization-considerations.Rmd’

--- re-building ‘timing-experiments.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 156-169 (timing-experiments.Rmd) 
Error: processing vignette 'timing-experiments.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘timing-experiments.Rmd’

--- re-building ‘dtwclust.Rnw’ using knitr_notangle
Loading required package: cluster
Warning in tsclust(CharTraj[1L:20L], type = "h", k = 4L, distance = "dtw_basic",  :
  Distance matrix is not symmetric, and hierarchical clustering assumes it is (it ignores the upper triangular).
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: clue
--- finished re-building ‘dtwclust.Rnw’

SUMMARY: processing the following file failed:
  ‘timing-experiments.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘hdf5r’
Error(s) in re-building vignettes:
--- re-building ‘dub-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: DUBStepR
Attaching SeuratObject

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 63-65 (dub-vignette.Rmd) 
Error: processing vignette 'dub-vignette.Rmd' failed with diagnostics:
Please install hdf5r to read HDF5 files
--- failed re-building ‘dub-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 194.2Mb
  sub-directories of 1Mb or more:
    libs  193.9Mb
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    doc    1.7Mb
    libs  30.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Error(s) in re-building vignettes:
--- re-building ‘plotting-a-toy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  no font could be found for family "Arial"
Quitting from lines 49-50 (plotting-a-toy.Rmd) 
Error: processing vignette 'plotting-a-toy.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘plotting-a-toy.Rmd’

SUMMARY: processing the following file failed:
  ‘plotting-a-toy.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   3.0Mb
Running ‘testthat.R’ [67s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   7.       └─base:::tryCatchList(expr, classes, parentenv, handlers)
   8.         └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.           └─value[[3L]](cond)
  ── Error (test-h5.R:39:3): errors gracefully ───────────────────────────────────
  Error: there is no package called 'hdf5r'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-h5.R:39:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 3 | WARN 2 | SKIP 0 | PASS 545 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘functionality.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 93-109 (functionality.Rmd) 
Error: processing vignette 'functionality.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘functionality.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘eaf/libs/eaf.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘eaf/io.o’, ‘mo-tools/hv.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘eaf/io.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs       10.1Mb
    shiny_app   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘earlyR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 42-48 (earlyR.Rmd) 
Error: processing vignette 'earlyR.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘earlyR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   4.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ebayesthresh.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 49-60 (ebayesthresh.Rmd) 
Error: processing vignette 'ebayesthresh.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ebayesthresh.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘how_to_use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: MASS

'drc' has been loaded.

Please cite R and 'drc' if used for a publication,
for references type 'citation()' and 'citation('drc')'.


Attaching package: 'drc'

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

    gaussian, getInitial


Attaching package: 'dplyr'

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

    select

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 41-48 (how_to_use.Rmd) 
Error: processing vignette 'how_to_use.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘how_to_use.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ecap-demo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: splines
Loading required package: quadprog
Loading required package: ggplot2
Quitting from lines 90-91 (ecap-demo.Rmd) 
Error: processing vignette 'ecap-demo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ecap-demo.Rmd’

SUMMARY: processing the following file failed:
  ‘ecap-demo.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Error: package or namespace load failed for ‘echarty’:
 .onLoad failed in loadNamespace() for 'echarty', details:
  call: loadNamespace(x)
  error: there is no package called ‘shiny’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘echo-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-100 (echo-vignette.Rmd) 
Error: processing vignette 'echo-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘echo-vignette.Rmd’

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

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

Package suggested but not available for checking: ‘ComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘convert.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘convert.Rmd’

--- re-building ‘create.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘create.Rmd’

--- re-building ‘use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 298-306 (use.Rmd) 
Error: processing vignette 'use.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘use.Rmd’

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

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

> ### Name: ecospat.maxentvarimport
> ### Title: Maxent Variable Importance
> ### Aliases: ecospat.maxentvarimport
> 
> ### ** Examples
> 
> library(dismo)
Loading required package: raster

Attaching package: ‘raster’

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

    rotate, zoom

> data('ecospat.testData')
> 
> # data for Soldanella alpina
> data.Solalp<- ecospat.testData[c("Soldanella_alpina","ddeg","mind","srad","slp","topo")]
> 
> # copy maxent.jar file in the right folder
> path.from<-system.file("extdata", "maxent.txt", package="ecospat")
> path.to <- paste0(system.file(package="dismo"), "/java/maxent.txt")
> path.to.renamed <- paste0(system.file(package="dismo"), "/java/maxent.jar")
> file.copy(path.from,path.to,overwrite = TRUE)
[1] TRUE
> file.rename(path.to, path.to.renamed)
[1] TRUE
> 
> if (file.exists(path.to.renamed) & require(rJava)) {
+   me <- maxent(data.Solalp[,-1],data.Solalp[,1])
+   ecospat.maxentvarimport (model=me, dfvar=data.Solalp[,-1], nperm=5)
+   }
Loading required package: rJava
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 36-42 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EDA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 128-141 (EDA.Rmd) 
Error: processing vignette 'EDA.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘EDA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘filters.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘filters.Rmd’

--- re-building ‘metrics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 41-44 (metrics.Rmd) 
Error: processing vignette 'metrics.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘metrics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘edfReaderVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 434-470 (edfReaderVignette.Rmd) 
Error: processing vignette 'edfReaderVignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘edfReaderVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘edgarWebR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 119-122 (edgarWebR.Rmd) 
Error: processing vignette 'edgarWebR.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘edgarWebR.Rmd’

--- re-building ‘parsing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: testthat
--- finished re-building ‘parsing.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EDOIF_demo.Rmd’ using knitr
Quitting from lines 54-55 (EDOIF_demo.Rmd) 
Error: processing vignette 'EDOIF_demo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘EDOIF_demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘eechidna-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 86-105 (eechidna-intro.Rmd) 
Error: processing vignette 'eechidna-intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘eechidna-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [4s/5s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
   24. │     └─grid::pushViewport(vp, recording = FALSE)
   25. │       └─base::lapply(vps, push.vp, recording)
   26. │         ├─grid:::FUN(X[[i]], ...)
   27. │         └─grid:::push.vp.vpTree(X[[i]], ...)
   28. │           ├─grid:::push.vp(vp$parent, recording)
   29. │           └─grid:::push.vp.viewport(vp$parent, recording)
   30. │             └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   31. └─(function (x) ...
   32.   ├─grid::widthDetails(x)
   33.   └─grid:::widthDetails.text(x)
   34.     └─grid:::grid.Call(...)
  
  [ FAIL 1 | WARN 224 | SKIP 0 | PASS 506 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Quitting from lines 170-173 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘eesim.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

This is dlnm 2.4.6. For details: help(dlnm) and vignette('dlnmOverview').
`geom_smooth()` using formula 'y ~ x'
Quitting from lines 35-50 (eesim.Rmd) 
Error: processing vignette 'eesim.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘eesim.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.1Mb
Packages required but not available: 'pcalg', 'RBGL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ega.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-30 (ega.Rmd) 
Error: processing vignette 'ega.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ega.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 106.5Mb
  sub-directories of 1Mb or more:
    libs  105.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Ecosystem.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Quitting from lines 38-54 (Ecosystem.Rmd) 
Error: processing vignette 'Ecosystem.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Ecosystem.Rmd’

--- re-building ‘Overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: gridExtra
Loading required package: ggplot2
Quitting from lines 33-46 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following files failed:
  ‘Ecosystem.Rmd’ ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(EGRETci)
  > test_check("EGRETci")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (10)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (tests_boot_tests.R:112:3): paVector ────────────────────────────────
  `paIndexWinter` not equal to 11:13.
  Lengths differ: 4 is not 3
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ehr_vignette_01_mxr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 287-299 (ehr_vignette_01_mxr.Rmd) 
Error: processing vignette 'ehr_vignette_01_mxr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ehr_vignette_01_mxr.Rmd’

--- re-building ‘ehr_vignette_02_str.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘ehr_vignette_02_str.Rmd’

--- re-building ‘ehr_vignette_03_DoseBuilding.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘ehr_vignette_03_DoseBuilding.Rmd’

--- re-building ‘ehr_vignette_04_Build_PK_Oral.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘ehr_vignette_04_Build_PK_Oral.Rmd’

SUMMARY: processing the following file failed:
  ‘ehr_vignette_01_mxr.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘BiocStyle’
installed size is 100.9Mb
  sub-directories of 1Mb or more:
    libs  100.7Mb
Error(s) in re-building vignettes:
--- re-building ‘DataAnalysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘DataAnalysis.Rmd’

--- re-building ‘IndependenceExploration.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘IndependenceExploration.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 120-123 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 49.8Mb
  sub-directories of 1Mb or more:
    libs  48.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘EIX.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
   [[ suppressing 19 column names 'satisfaction_level', 'last_evaluation', 'number_project' ... ]]
Quitting from lines 68-76 (EIX.Rmd) 
Error: processing vignette 'EIX.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘EIX.Rmd’

--- re-building ‘titanic_data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 49-51 (titanic_data.Rmd) 
Error: processing vignette 'titanic_data.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘titanic_data.Rmd’

SUMMARY: processing the following files failed:
  ‘EIX.Rmd’ ‘titanic_data.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘nba-example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 42-48 (nba-example.Rmd) 
Error: processing vignette 'nba-example.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘nba-example.Rmd’

SUMMARY: processing the following file failed:
  ‘nba-example.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/ELT.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘showtext’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.6Mb
Package suggested but not available for checking: ‘R2jags’
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  19.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.8Mb
Packages required but not available: 'showtext', 'sysfonts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘EmpiricalCiCalibrationVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 72-74 (EmpiricalCiCalibrationVignette.Rmd) 
Error: processing vignette 'EmpiricalCiCalibrationVignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘EmpiricalCiCalibrationVignette.Rmd’

--- re-building ‘EmpiricalPCalibrationVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 52-53 (EmpiricalPCalibrationVignette.Rmd) 
Error: processing vignette 'EmpiricalPCalibrationVignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘EmpiricalPCalibrationVignette.Rmd’

SUMMARY: processing the following files failed:
  ‘EmpiricalCiCalibrationVignette.Rmd’
  ‘EmpiricalPCalibrationVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'DESeq2', 'GenomicRanges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/emstreeR.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘enpls.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 65-76 (enpls.Rmd) 
Error: processing vignette 'enpls.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘enpls.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘enrichR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 90-91 (enrichR.Rmd) 
Error: processing vignette 'enrichR.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘enrichR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GLMs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-69 (GLMs.Rmd) 
Error: processing vignette 'GLMs.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘GLMs.Rmd’

--- re-building ‘bias.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘bias.Rmd’

--- re-building ‘exponential_family.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘exponential_family.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/EnsembleBase.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/EnsembleCV.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/EnsemblePCReg.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/EnsemblePenReg.Rcheck/00install.out’ for details.
Package required but not available: ‘DECIPHER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘entropart.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 53-55 (entropart.Rmd) 
Error: processing vignette 'entropart.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘entropart.Rmd’

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

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

Packages suggested but not available for checking: 'xcms', 'MSnbase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   4.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘eoffice.Rmd’ using knitr
Quitting from lines 63-94 (eoffice.Rmd) 
Error: processing vignette 'eoffice.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘eoffice.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epca.Rmd’ using knitr
Quitting from lines 137-149 (epca.Rmd) 
Error: processing vignette 'epca.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘epca.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘epicontacts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘epicontacts.Rmd’

--- re-building ‘epicontacts_class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
--- finished re-building ‘epicontacts_class.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘EpiCurve.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: ISOweek
Loading required package: scales
Quitting from lines 103-106 (EpiCurve.Rmd) 
Error: processing vignette 'EpiCurve.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘EpiCurve.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘demo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 67-69 (demo.Rmd) 
Error: processing vignette 'demo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘fitting.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 65-79 (fitting.Rmd) 
Error: processing vignette 'fitting.Rmd' failed with diagnostics:
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--- failed re-building ‘fitting.Rmd’

--- re-building ‘simulation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 73-85 (simulation.Rmd) 
Error: processing vignette 'simulation.Rmd' failed with diagnostics:
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--- failed re-building ‘simulation.Rmd’

SUMMARY: processing the following files failed:
  ‘fitting.Rmd’ ‘simulation.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epiflows-class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 108-117 (epiflows-class.Rmd) 
Error: processing vignette 'epiflows-class.Rmd' failed with diagnostics:
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--- failed re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-70 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘epiflows-class.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 147.9Mb
  sub-directories of 1Mb or more:
    libs  146.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘defs-and-eqns.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘defs-and-eqns.Rmd’

--- re-building ‘epiphy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 84-85 (epiphy.Rmd) 
Error: processing vignette 'epiphy.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘epiphy.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.1Mb
    libs   2.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ERSA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 107-110 (ERSA.Rmd) 
Error: processing vignette 'ERSA.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ERSA.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ESTER.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 95-102 (ESTER.Rmd) 
Error: processing vignette 'ESTER.Rmd' failed with diagnostics:
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--- failed re-building ‘ESTER.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Testing-estimators-with-EstimDiagnostics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 44-46 (Testing-estimators-with-EstimDiagnostics.Rmd) 
Error: processing vignette 'Testing-estimators-with-EstimDiagnostics.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Testing-estimators-with-EstimDiagnostics.Rmd’

SUMMARY: processing the following file failed:
  ‘Testing-estimators-with-EstimDiagnostics.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘RODBC’
Error(s) in re-building vignettes:
  ...
--- re-building ‘msfc_forward_curve.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 55-56 (msfc_forward_curve.Rmd) 
Error: processing vignette 'msfc_forward_curve.Rmd' failed with diagnostics:
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--- failed re-building ‘msfc_forward_curve.Rmd’

--- re-building ‘portfolio_insurance_strategies.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 53-66 (portfolio_insurance_strategies.Rmd) 
Error: processing vignette 'portfolio_insurance_strategies.Rmd' failed with diagnostics:
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--- failed re-building ‘portfolio_insurance_strategies.Rmd’

SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Eunomia.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/EvidenceSynthesis.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.9Mb
Error(s) in re-building vignettes:
--- re-building ‘UsingEvolutionaryGames.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 204-207 (UsingEvolutionaryGames.Rmd) 
Error: processing vignette 'UsingEvolutionaryGames.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘UsingEvolutionaryGames.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 40.2Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    exiftool  14.0Mb
Packages required but not available:
  'Rsamtools', 'GenomicRanges', 'GenomicAlignments'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘ExPanD_notebook.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 181-188 (ExPanD_notebook.Rmd) 
Error: processing vignette 'ExPanD_notebook.Rmd' failed with diagnostics:
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--- failed re-building ‘ExPanD_notebook.Rmd’

--- re-building ‘ExPanDaR-functions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 77-78 (ExPanDaR-functions.Rmd) 
Error: processing vignette 'ExPanDaR-functions.Rmd' failed with diagnostics:
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--- failed re-building ‘ExPanDaR-functions.Rmd’

--- re-building ‘customize_ExPanD.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘customize_ExPanD.Rmd’

--- re-building ‘use_ExPanD.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘use_ExPanD.Rmd’

SUMMARY: processing the following files failed:
  ‘ExPanD_notebook.Rmd’ ‘ExPanDaR-functions.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘exploreR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 69-71 (exploreR.Rmd) 
Error: processing vignette 'exploreR.Rmd' failed with diagnostics:
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--- failed re-building ‘exploreR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/extraTrees.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: eyelinker
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: tidyr
Loading required package: ggplot2
Loading required package: intervals

Attaching package: 'intervals'

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

    expand

Loading required package: stringr
Quitting from lines 133-135 (basics.Rmd) 
Error: processing vignette 'basics.Rmd' failed with diagnostics:
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--- failed re-building ‘basics.Rmd’

--- re-building ‘format.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: eyelinker
--- finished re-building ‘format.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ezcox.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 104-109 (ezcox.Rmd) 
Error: processing vignette 'ezcox.Rmd' failed with diagnostics:
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--- failed re-building ‘ezcox.Rmd’

--- re-building ‘ezforest.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 22-34 (ezforest.Rmd) 
Error: processing vignette 'ezforest.Rmd' failed with diagnostics:
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--- failed re-building ‘ezforest.Rmd’

--- re-building ‘ezgroup.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 23-27 (ezgroup.Rmd) 
Error: processing vignette 'ezgroup.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ezgroup.Rmd’

SUMMARY: processing the following files failed:
  ‘ezcox.Rmd’ ‘ezforest.Rmd’ ‘ezgroup.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ezEDA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 87-90 (ezEDA.Rmd) 
Error: processing vignette 'ezEDA.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ezEDA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 39-41 (basics.Rmd) 
Error: processing vignette 'basics.Rmd' failed with diagnostics:
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--- failed re-building ‘basics.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 35-36 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following files failed:
  ‘basics.Rmd’ ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

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

    interval

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

    date, intersect, setdiff, union

`summarise()` has grouped output by 'month'. You can override using the `.groups` argument.
Quitting from lines 63-65 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘fable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: fabletools

Attaching package: 'tsibble'

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

    intersect, setdiff, union


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 40-42 (fable.Rmd) 
Error: processing vignette 'fable.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘fable.Rmd’

--- re-building ‘transformations.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘transformations.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘building_a_factory.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-50 (building_a_factory.Rmd) 
Error: processing vignette 'building_a_factory.Rmd' failed with diagnostics:
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--- failed re-building ‘building_a_factory.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘fairness.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 310-311 (fairness.Rmd) 
Error: processing vignette 'fairness.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘fairness.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro-faq.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (Intro-faq.Rmd) 
Error: processing vignette 'Intro-faq.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Intro-faq.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro-faq.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   3.9Mb
installed size is  6.1Mb
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    data   3.1Mb
    libs   2.9Mb
installed size is  9.4Mb
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    libs   9.2Mb
installed size is 43.8Mb
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installed size is  7.6Mb
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    libs   7.2Mb
installed size is 17.7Mb
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    data   1.3Mb
    libs  16.3Mb
installed size is  8.7Mb
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    data   5.3Mb
    libs   3.1Mb
installed size is  9.7Mb
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    libs   9.6Mb
installed size is 18.3Mb
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    libs  18.2Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data  16.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.6Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.9Mb
Package suggested but not available for checking: ‘DESeq2’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.9Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignettes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 178-185 (vignettes.Rmd) 
Error: processing vignette 'vignettes.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vignettes.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is 41.4Mb
  sub-directories of 1Mb or more:
    libs  39.8Mb
installed size is 90.8Mb
  sub-directories of 1Mb or more:
    libs  90.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.8Mb
Error(s) in re-building vignettes:
--- re-building ‘feasts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: fabletools

Attaching package: 'tsibble'

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

    intersect, setdiff, union


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 40-42 (feasts.Rmd) 
Error: processing vignette 'feasts.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘feasts.Rmd’

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

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

> ### Name: saveTree
> ### Title: saveTree
> ### Aliases: saveTree
> ### Keywords: saveTree
> 
> ### ** Examples
> 
> 
> require(featurefinder)
> data(examples)
> fit1=saveTree(data,vars,expr,i,outputPath=tempdir(),runname,mainfaclevels[1],
+      treeGenerationMinBucket)
[1] 50
Warning in graphics::mtext(sprintf("help(\"%s\")", nameEx()), side = 4,  :
  no font could be found for family "Arial"
Warning in graphics::mtext(sprintf("help(\"%s\")", nameEx()), side = 4,  :
  no font could be found for family "Arial"
Warning in graphics::mtext(sprintf("help(\"%s\")", nameEx()), side = 4,  :
  no font could be found for family "Arial"
Warning in graphics::mtext(sprintf("help(\"%s\")", nameEx()), side = 4,  :
  no font could be found for family "Arial"
Warning in graphics::mtext(sprintf("help(\"%s\")", nameEx()), side = 4,  :
  no font could be found for family "Arial"
Warning in strwidth(s[i], units[i], cex[i], font[i], vfont = NULL) :
  no font could be found for family "Arial"
Warning in strheight(s[i], units[i], cex[i], font[i], vfont = NULL) :
  no font could be found for family "Arial"
Warning in strheight(s[i], units[i], cex[i], font[i], vfont = NULL) :
  no font could be found for family "Arial"
Warning in strwidth(s[i], units[i], cex[i], font[i], vfont = NULL) :
  no font could be found for family "Arial"
Error in if (all(r == 0)) { : missing value where TRUE/FALSE needed
Calls: saveTree ... <Anonymous> -> prp -> draw.labs -> draw.boxes -> rounded.rect
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘feature_terminatoR_howto.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: lattice
Loading required package: ggplot2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    combine

The following object is masked from 'package:ggplot2':

    margin

Quitting from lines 137-140 (feature_terminatoR_howto.Rmd) 
Error: processing vignette 'feature_terminatoR_howto.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘feature_terminatoR_howto.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘fec_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "cand_id"
`summarise()` has grouped output by 'cand_id'. You can override using the `.groups` argument.
Quitting from lines 138-151 (fec_vignette.Rmd) 
Error: processing vignette 'fec_vignette.Rmd' failed with diagnostics:
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--- failed re-building ‘fec_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/fedmatch.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘feisr-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 191-210 (feisr-vignette.Rmd) 
Error: processing vignette 'feisr-vignette.Rmd' failed with diagnostics:
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--- failed re-building ‘feisr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 48-51 (basic.Rmd) 
Error: processing vignette 'basic.Rmd' failed with diagnostics:
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--- failed re-building ‘basic.Rmd’

--- re-building ‘custom.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘custom.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
  ...
--- re-building ‘firebehavioR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 97-103 (firebehavioR.Rmd) 
Error: processing vignette 'firebehavioR.Rmd' failed with diagnostics:
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--- failed re-building ‘firebehavioR.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Data-Model.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dm'

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

    filter

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 36-39 (Data-Model.Rmd) 
Error: processing vignette 'Data-Model.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Data-Model.Rmd’

--- re-building ‘fishdata-examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

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

    intersect, setdiff, setequal, union

Quitting from lines 32-40 (fishdata-examples.Rmd) 
Error: processing vignette 'fishdata-examples.Rmd' failed with diagnostics:
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--- failed re-building ‘fishdata-examples.Rmd’

SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 46.9Mb
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installed size is 36.2Mb
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    libs  23.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbitScraper-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.6Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘how_to_flair.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines NA-6 (how_to_flair.Rmd) 
Error: processing vignette 'how_to_flair.Rmd' failed with diagnostics:
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--- failed re-building ‘how_to_flair.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
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installed size is  9.1Mb
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Error(s) in re-building vignettes:
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--- re-building ‘Intro-flashCard.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-32 (Intro-flashCard.Rmd) 
Error: processing vignette 'Intro-flashCard.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Intro-flashCard.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 107.2Mb
  sub-directories of 1Mb or more:
    libs  106.6Mb
Package required and available but unsuitable version: ‘officer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
installed size is 27.4Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
  ...
--- re-building ‘fma-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
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Error: processing vignette 'fma-vignette.Rmd' failed with diagnostics:
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--- failed re-building ‘fma-vignette.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 55.6Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 138-141 (basics.Rmd) 
Error: processing vignette 'basics.Rmd' failed with diagnostics:
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--- failed re-building ‘basics.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_fontHind.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 38-49 (Using_fontHind.Rmd) 
Error: processing vignette 'Using_fontHind.Rmd' failed with diagnostics:
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--- failed re-building ‘Using_fontHind.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_fontMPlus.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 56-67 (Using_fontMPlus.Rmd) 
Error: processing vignette 'Using_fontMPlus.Rmd' failed with diagnostics:
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--- failed re-building ‘Using_fontMPlus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘minet’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Foodingraph_quickstart.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 148-150 (Foodingraph_quickstart.Rmd) 
Error: processing vignette 'Foodingraph_quickstart.Rmd' failed with diagnostics:
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--- failed re-building ‘Foodingraph_quickstart.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘forcats.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 31-34 (forcats.Rmd) 
Error: processing vignette 'forcats.Rmd' failed with diagnostics:
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--- failed re-building ‘forcats.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
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    libs   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_ForecastTB.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-63 (Introduction_to_ForecastTB.Rmd) 
Error: processing vignette 'Introduction_to_ForecastTB.Rmd' failed with diagnostics:
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--- failed re-building ‘Introduction_to_ForecastTB.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘forestplot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: grid
Loading required package: magrittr
Loading required package: checkmate
Quitting from lines 56-89 (forestplot.Rmd) 
Error: processing vignette 'forestplot.Rmd' failed with diagnostics:
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--- failed re-building ‘forestplot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
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    data   1.0Mb
    libs   8.3Mb
Error(s) in re-building vignettes:
--- re-building ‘Overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: xtable

Attaching package: 'likert'

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

    recode

Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Quitting from lines 55-61 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fourierin_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-83 (fourierin_details.Rmd) 
Error: processing vignette 'fourierin_details.Rmd' failed with diagnostics:
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--- failed re-building ‘fourierin_details.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Exporting_graphs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Exporting_graphs.Rmd’

--- re-building ‘fplot_walkthrough.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 100-103 (fplot_walkthrough.Rmd) 
Error: processing vignette 'fplot_walkthrough.Rmd' failed with diagnostics:
invalid '(to - from)/by'
--- failed re-building ‘fplot_walkthrough.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2', 'Rsymphony'
installed size is 11.2Mb
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    R      2.0Mb
    help   2.2Mb
    libs   5.4Mb
Error(s) in re-building vignettes:
--- re-building ‘basic_usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Quitting from lines 59-61 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
'This file was created by CMPT_ME_BEME_OP_INV_RETS using the 202105 CRSP database.' does not exist in current working directory ('/Volumes/Builds/packages/big-sur-arm64/results/4.1/frenchdata.Rcheck/vign_test/frenchdata/vignettes').
--- failed re-building ‘basic_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   8.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R   6.0Mb
installed size is 107.2Mb
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    data   5.5Mb
    doc    1.5Mb
    help   1.4Mb
    libs  97.8Mb
installed size is 51.8Mb
  sub-directories of 1Mb or more:
    libs  51.4Mb
Package suggested but not available for checking: ‘foba’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/fsdaR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/FSelector.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(entropy)
  
  Attaching package: 'entropy'
  
  The following object is masked from 'package:FSelectorRcpp':
  
      discretize
  
  > library(lintr)
  > 
  > test_check("FSelectorRcpp")
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/fstcore.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/fst.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘funModeling_quickstart.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

funModeling v.1.9.4 :)
Examples and tutorials at livebook.datascienceheroes.com
 / Now in Spanish: librovivodecienciadedatos.ai
Quitting from lines 79-80 (funModeling_quickstart.Rmd) 
Error: processing vignette 'funModeling_quickstart.Rmd' failed with diagnostics:
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--- failed re-building ‘funModeling_quickstart.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 61-74 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
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--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘new_distinctiveness.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 131-139 (new_distinctiveness.Rmd) 
Error: processing vignette 'new_distinctiveness.Rmd' failed with diagnostics:
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--- failed re-building ‘new_distinctiveness.Rmd’

--- re-building ‘rarity_indices.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 281-341 (rarity_indices.Rmd) 
Error: processing vignette 'rarity_indices.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘rarity_indices.Rmd’

--- re-building ‘sparse_matrices.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sparse_matrices.Rmd’

SUMMARY: processing the following files failed:
  ‘new_distinctiveness.Rmd’ ‘rarity_indices.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘beales.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘beales.Rmd’

--- re-building ‘trendtests.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 52-63 (trendtests.Rmd) 
Error: processing vignette 'trendtests.Rmd' failed with diagnostics:
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--- failed re-building ‘trendtests.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘subgroup_fusion.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 87-98 (subgroup_fusion.Rmd) 
Error: processing vignette 'subgroup_fusion.Rmd' failed with diagnostics:
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--- failed re-building ‘subgroup_fusion.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘FusionLearn.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 231-247 (FusionLearn.Rmd) 
Error: processing vignette 'FusionLearn.Rmd' failed with diagnostics:
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--- failed re-building ‘FusionLearn.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘000.sessionDetails.R’ [0s/0s]
  Running ‘ClusterRegistry.R’ [1s/2s]
  Running ‘Future-class.R’ [1s/1s]
  Running ‘FutureError.R’ [0s/0s]
  Running ‘FutureGlobals.R’ [0s/0s]
  Running ‘FutureRegistry.R’ [0s/1s]
  Running ‘backtrace.R’ [1s/2s]
  Running ‘cluster-missing-future-pkg.R’ [0s/1s]
  Running ‘cluster.R’ [1s/7s]
Running the tests in ‘tests/cluster.R’ failed.
Last 13 lines of output:
  > ## Sanity checks
  > pid2 <- Sys.getpid()
  > message("Main PID (original): ", pid)
  Main PID (original): 180
  > message("Main PID: ", pid2)
  Main PID: 180
  > stopifnot(pid2 == pid)
  > 
  > source("incl/end.R")
  > 
  > ## Sanity checks
  > pid2 <- Sys.getpid()
  > message("Main PID (original): ", pid)
  Error in message("Main PID (original): ", pid) : object 'pid' not found
  Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fuzzyreg)
  > 
  > test_check("fuzzyreg")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_correctSolution.R:50:3): correct TEF for crisp numbers ────────
  0 not equal to TEF(f).
  1/1 mismatches
  [1] 0 - 3 == -3
  
  [ FAIL 1 | WARN 8 | SKIP 0 | PASS 24 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/G2Sd.Rcheck/00install.out’ for details.
Package required but not available: ‘rtracklayer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘doserate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 72-74 (doserate.Rmd) 
Error: processing vignette 'doserate.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘doserate.Rmd’

--- re-building ‘gamma.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 77-80 (gamma.Rmd) 
Error: processing vignette 'gamma.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gamma.Rmd’

SUMMARY: processing the following files failed:
  ‘doserate.Rmd’ ‘gamma.Rmd’

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘doMPI’
Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: reshape2
Quitting from lines 36-38 (simple_example.Rmd) 
Error: processing vignette 'simple_example.Rmd' failed with diagnostics:
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--- failed re-building ‘simple_example.Rmd’

--- re-building ‘tcga_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 43-45 (tcga_example.Rmd) 
Error: processing vignette 'tcga_example.Rmd' failed with diagnostics:
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--- failed re-building ‘tcga_example.Rmd’

SUMMARY: processing the following files failed:
  ‘simple_example.Rmd’ ‘tcga_example.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 49.9Mb
  sub-directories of 1Mb or more:
    doc   44.4Mb
    libs   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gasper_vignette.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
Content type 'application/x-tar' length 3211 bytes
==================================================
downloaded 3211 bytes

Quitting from lines 81-84 (gasper_vignette.rmd) 
Error: processing vignette 'gasper_vignette.rmd' failed with diagnostics:
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--- failed re-building ‘gasper_vignette.rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  11.5Mb
installed size is 94.6Mb
  sub-directories of 1Mb or more:
    libs  94.1Mb
installed size is 69.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     66.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘fit_gaussian_2D.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-61 (fit_gaussian_2D.Rmd) 
Error: processing vignette 'fit_gaussian_2D.Rmd' failed with diagnostics:
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--- failed re-building ‘fit_gaussian_2D.Rmd’

--- re-building ‘formulas-used-by-fit-gaussian-2D.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘formulas-used-by-fit-gaussian-2D.Rmd’

--- re-building ‘troubleshooting-model-fits.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘troubleshooting-model-fits.Rmd’

SUMMARY: processing the following file failed:
  ‘fit_gaussian_2D.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/gdalcubes.Rcheck/00install.out’ for details.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.4Mb
    libs      1.7Mb
Packages required but not available: 'ggtree', 'ShortRead'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R  11.0Mb
Package required but not available: ‘GEOquery’

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

Package suggested but not available for checking: ‘RHugin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Found the following significant warnings:
  hal.cpp:266:10: warning: 'sem_init' is deprecated [-Wdeprecated-declarations]
  hal.cpp:271:13: warning: 'sem_destroy' is deprecated [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/GENLIB.Rcheck/00install.out’ for details.
Package required but not available: ‘GenomicRanges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   5.1Mb
Package required but not available: ‘reactome.db’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 111-112 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘geofacet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-64 (geofacet.Rmd) 
Error: processing vignette 'geofacet.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘geofacet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 139.7Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    libs  138.4Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   6.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   5.6Mb
Error(s) in re-building vignettes:
--- re-building ‘Merging_Election_Data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

To enable 
caching of data, set `options(tigris_use_cache = TRUE)` in your R script or .Rprofile.
Linking to GEOS 3.9.1, GDAL 3.2.3, PROJ 7.2.1
--- finished re-building ‘Merging_Election_Data.Rmd’

--- re-building ‘Redistricting_School_Districts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'redist'

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

    filter

Linking to GEOS 3.9.1, GDAL 3.2.3, PROJ 7.2.1
To enable 
caching of data, set `options(tigris_use_cache = TRUE)` in your R script or .Rprofile.
Quitting from lines 71-74 (Redistricting_School_Districts.Rmd) 
Error: processing vignette 'Redistricting_School_Districts.Rmd' failed with diagnostics:
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--- failed re-building ‘Redistricting_School_Districts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘udunits2’
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R         9.0Mb
    extdata   1.6Mb
Package required but not available: ‘cqn’

Packages suggested but not available for checking:
  'DESeq2', 'ChAMP', 'clusterProfiler', 'org.Hs.eg.db', 'edgeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: Matrix
Loaded glmnet 4.1-2
Quitting from lines 277-294 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
'from' must be a finite number
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gld_vignette-ReadLattes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 85-93 (gld_vignette-ReadLattes.Rmd) 
Error: processing vignette 'gld_vignette-ReadLattes.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gld_vignette-ReadLattes.Rmd’

SUMMARY: processing the following file failed:
  ‘gld_vignette-ReadLattes.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [27s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   22. │     └─grid::pushViewport(vp, recording = FALSE)
   23. │       └─base::lapply(vps, push.vp, recording)
   24. │         ├─grid:::FUN(X[[i]], ...)
   25. │         └─grid:::push.vp.vpTree(X[[i]], ...)
   26. │           ├─grid:::push.vp(vp$parent, recording)
   27. │           └─grid:::push.vp.viewport(vp$parent, recording)
   28. │             └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   29. └─(function (x) ...
   30.   ├─grid::widthDetails(x)
   31.   └─grid:::widthDetails.text(x)
   32.     └─grid:::grid.Call(...)
  
  [ FAIL 1 | WARN 72 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gtdd-vignette_GetTDData.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 44-49 (gtdd-vignette_GetTDData.Rmd) 
Error: processing vignette 'gtdd-vignette_GetTDData.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gtdd-vignette_GetTDData.Rmd’

--- re-building ‘gtdd-vignette_YieldCurve.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘gtdd-vignette_YieldCurve.Rmd’

SUMMARY: processing the following file failed:
  ‘gtdd-vignette_GetTDData.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘RGtk2’
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  36.6Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   22. │     └─grid::pushViewport(vp, recording = FALSE)
   23. │       └─base::lapply(vps, push.vp, recording)
   24. │         ├─grid:::FUN(X[[i]], ...)
   25. │         └─grid:::push.vp.vpTree(X[[i]], ...)
   26. │           ├─grid:::push.vp(vp$parent, recording)
   27. │           └─grid:::push.vp.viewport(vp$parent, recording)
   28. │             └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   29. └─(function (x) ...
   30.   ├─grid::widthDetails(x)
   31.   └─grid:::widthDetails.text(x)
   32.     └─grid:::grid.Call(...)
  
  [ FAIL 5 | WARN 33 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ggalluvial.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Quitting from lines 36-46 (ggalluvial.rmd) 
Error: processing vignette 'ggalluvial.rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggalluvial.rmd’

--- re-building ‘labels.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 32-41 (labels.rmd) 
Error: processing vignette 'labels.rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘labels.rmd’

--- re-building ‘order-rectangles.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 43-46 (order-rectangles.rmd) 
Error: processing vignette 'order-rectangles.rmd' failed with diagnostics:
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--- failed re-building ‘order-rectangles.rmd’

--- re-building ‘shiny.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 52-63 (shiny.Rmd) 
Error: processing vignette 'shiny.Rmd' failed with diagnostics:
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--- failed re-building ‘shiny.Rmd’

SUMMARY: processing the following files failed:
  ‘ggalluvial.rmd’ ‘labels.rmd’ ‘order-rectangles.rmd’ ‘shiny.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [28s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  +   library(testthat)
  +   library(GGally)
  + 
  +   test_check("GGally")
  + }
  Loading required package: ggplot2
  Registered S3 method overwritten by 'GGally':
    method from   
    +.gg   ggplot2
  # weights:  24 (14 variable)
  initial  value 50552.644463 
  iter  10 value 45030.930814
  iter  20 value 43102.145726
  final  value 43101.422966 
  converged
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggalt_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 33-71 (ggalt_examples.Rmd) 
Error: processing vignette 'ggalt_examples.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggalt_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-anim_save.R:22:3): anim_save overwrites existing files ────────
  `frames_1` not equal to 2.
  1/1 mismatches
  [1] 1 - 2 == -1
  ── Failure (test-anim_save.R:28:3): anim_save overwrites existing files ────────
  `frames_2` not equal to 3.
  1/1 mismatches
  [1] 1 - 3 == -2
  
  [ FAIL 2 | WARN 48 | SKIP 1 | PASS 5 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gganimate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 38-45 (gganimate.Rmd) 
Error: processing vignette 'gganimate.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gganimate.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ggasym-corrr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 81-88 (ggasym-corrr.Rmd) 
Error: processing vignette 'ggasym-corrr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggasym-corrr.Rmd’

--- re-building ‘ggasym-stats.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 89-93 (ggasym-stats.Rmd) 
Error: processing vignette 'ggasym-stats.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggasym-stats.Rmd’

SUMMARY: processing the following files failed:
  ‘ggasym-corrr.Rmd’ ‘ggasym-stats.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-ggconf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 22-24 (Introduction-to-ggconf.Rmd) 
Error: processing vignette 'Introduction-to-ggconf.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction-to-ggconf.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-ggconf.Rmd’

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

> ### Name: geom_arima
> ### Title: ARIMA model
> ### Aliases: geom_arima
> 
> ### ** Examples
> 
> p_sa_ipi_fr <- ggplot(data = ipi_c_eu_df, mapping = aes(x = date, y = FR)) +
+     geom_line() +
+     labs(title = "Seasonal adjustment of the French industrial production index",
+          x = "time", y = NULL) +
+     geom_sa(color = "red", message = FALSE)
>          
> # To add the ARIMA model
> p_sa_ipi_fr + 
+     geom_arima(geom = "label",
+                x_arima = - Inf, y_arima = -Inf, 
+                vjust = -1, hjust = -0.1,
+                message = FALSE)
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggdendro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 54-56 (ggdendro.Rmd) 
Error: processing vignette 'ggdendro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggdendro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘posterior’
Error(s) in re-building vignettes:
  ...
--- re-building ‘shortcuts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 32-33 (shortcuts.Rmd) 
Error: processing vignette 'shortcuts.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘shortcuts.Rmd’

--- re-building ‘tests_and_coverage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tests_and_coverage.Rmd’

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

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

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: GGEBiplot -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggExtra.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 81-85 (ggExtra.Rmd) 
Error: processing vignette 'ggExtra.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggExtra.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-ggfittext.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-29 (introduction-to-ggfittext.Rmd) 
Error: processing vignette 'introduction-to-ggfittext.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction-to-ggfittext.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  20.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggformula.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 106-109 (ggformula.Rmd) 
Error: processing vignette 'ggformula.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggformula.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggfun.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 41-44 (ggfun.Rmd) 
Error: processing vignette 'ggfun.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggfun.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-gggenes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 37-43 (introduction-to-gggenes.Rmd) 
Error: processing vignette 'introduction-to-gggenes.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction-to-gggenes.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   27. │     └─grid::pushViewport(vp, recording = FALSE)
   28. │       └─base::lapply(vps, push.vp, recording)
   29. │         ├─grid:::FUN(X[[i]], ...)
   30. │         └─grid:::push.vp.vpTree(X[[i]], ...)
   31. │           ├─grid:::push.vp(vp$parent, recording)
   32. │           └─grid:::push.vp.viewport(vp$parent, recording)
   33. │             └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   34. └─(function (x) ...
   35.   ├─grid::widthDetails(x)
   36.   └─grid:::widthDetails.text(x)
   37.     └─grid:::grid.Call(...)
  
  [ FAIL 2 | WARN 32 | SKIP 0 | PASS 37 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gggibbous.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 10-30 (./gggibbous-content.txt) 
Quitting from lines 60-61 (./gggibbous-content.txt) 
Error: processing vignette 'gggibbous.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gggibbous.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 40-41 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Facets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 31-39 (Facets.Rmd) 
Error: processing vignette 'Facets.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Facets.Rmd’

--- re-building ‘Miscellaneous.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 29-49 (Miscellaneous.Rmd) 
Error: processing vignette 'Miscellaneous.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Miscellaneous.Rmd’

--- re-building ‘PositionGuides.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 29-34 (PositionGuides.Rmd) 
Error: processing vignette 'PositionGuides.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘PositionGuides.Rmd’

--- re-building ‘Statistics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 31-37 (Statistics.Rmd) 
Error: processing vignette 'Statistics.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Statistics.Rmd’

--- re-building ‘ggh4x.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-63 (ggh4x.Rmd) 
Error: processing vignette 'ggh4x.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggh4x.Rmd’

SUMMARY: processing the following files failed:
  ‘Facets.Rmd’ ‘Miscellaneous.Rmd’ ‘PositionGuides.Rmd’
  ‘Statistics.Rmd’ ‘ggh4x.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gghalves.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 40-42 (gghalves.Rmd) 
Error: processing vignette 'gghalves.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gghalves.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gghighlight.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 39-43 (gghighlight.Rmd) 
Error: processing vignette 'gghighlight.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gghighlight.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘package_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 102-111 (package_intro.Rmd) 
Error: processing vignette 'package_intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘package_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide-1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 178-181 (user-guide-1.Rmd) 
Error: processing vignette 'user-guide-1.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘user-guide-1.Rmd’

--- re-building ‘user-guide-2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 109-114 (user-guide-2.Rmd) 
Error: processing vignette 'user-guide-2.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘user-guide-2.Rmd’

SUMMARY: processing the following files failed:
  ‘user-guide-1.Rmd’ ‘user-guide-2.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ggip.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 93-99 (ggip.Rmd) 
Error: processing vignette 'ggip.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggip.Rmd’

--- re-building ‘visualizing-ip-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ipaddress
Quitting from lines 122-125 (visualizing-ip-data.Rmd) 
Error: processing vignette 'visualizing-ip-data.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘visualizing-ip-data.Rmd’

SUMMARY: processing the following files failed:
  ‘ggip.Rmd’ ‘visualizing-ip-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ggPredict.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
`geom_smooth()` using formula 'y ~ x'
Quitting from lines 38-40 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Loading required package: TH.data
Loading required package: survival
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

Loading required package: moonBook

Attaching package: 'moonBook'

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

    addLabelDf, getMapping

Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: Use of `longdf1[["variable"]]` is discouraged. Use `.data[["variable"]]` instead.
Warning: Use of `longdf2[["variable"]]` is discouraged. Use `.data[["variable"]]` instead.
Loading required package: gcookbook
--- finished re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
Running examples in ‘gglogo-Ex.R’ failed
The error most likely occurred in:

> ### Name: letterToPolygon
> ### Title: Convert an image file to a polygon
> ### Aliases: letterToPolygon
> 
> ### ** Examples
> 
> library(ggplot2)

Attaching package: ‘ggplot2’

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

    fortify

> letter <- letterToPolygon("R", fontfamily="Helvetica")
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Helvetica"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Helvetica"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Helvetica"
Error in `$<-.data.frame`(`*tmp*`, "order", value = 1L) : 
  replacement has 1 row, data has 0
Calls: letterToPolygon -> $<- -> $<-.data.frame
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gglogo-alphabet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'gglogo'

The following object is masked from 'package:ggplot2':

    fortify

Quitting from lines 32-36 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gglogo-alphabet.Rmd’

SUMMARY: processing the following file failed:
  ‘gglogo-alphabet.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 107-110 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Error(s) in re-building vignettes:
--- re-building ‘ggmosaic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'dplyr'

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

    combine

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 45-84 (ggmosaic.Rmd) 
Error: processing vignette 'ggmosaic.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggmosaic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggmuller.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-29 (ggmuller.Rmd) 
Error: processing vignette 'ggmuller.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggmuller.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ggnetwork.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

'network' 1.17.1 (2021-06-12), part of the Statnet Project
* 'news(package="network")' for changes since last version
* 'citation("network")' for citation information
* 'https://statnet.org' for help, support, and other information

Loading required package: statnet.common

Attaching package: 'statnet.common'

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

    attr, order

sna: Tools for Social Network Analysis
Version 2.6 created on 2020-10-5.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.

Quitting from lines 130-133 (ggnetwork.Rmd) 
Error: processing vignette 'ggnetwork.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggnetwork.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ggparty-graphic-partying.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 42-122 (ggparty-graphic-partying.Rmd) 
Error: processing vignette 'ggparty-graphic-partying.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggparty-graphic-partying.Rmd’

--- re-building ‘on-the-edge.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Quitting from lines 56-61 (on-the-edge.Rmd) 
Error: processing vignette 'on-the-edge.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘on-the-edge.Rmd’

SUMMARY: processing the following files failed:
  ‘ggparty-graphic-partying.Rmd’ ‘on-the-edge.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wraping-around-ggplot2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 36-40 (wraping-around-ggplot2.Rmd) 
Error: processing vignette 'wraping-around-ggplot2.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘wraping-around-ggplot2.Rmd’

SUMMARY: processing the following file failed:
  ‘wraping-around-ggplot2.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   1.9Mb
Error(s) in re-building vignettes:
--- re-building ‘model-based-annotations.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggpp
Loading required package: ggplot2

Attaching package: 'ggpp'

The following object is masked from 'package:ggplot2':

    annotate

Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'lubridate'

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

    date, intersect, setdiff, union


Attaching package: 'dplyr'

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

    first, last

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'nlme'

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

    collapse

Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve

Quitting from lines 128-133 (model-based-annotations.Rmd) 
Error: processing vignette 'model-based-annotations.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘model-based-annotations.Rmd’

SUMMARY: processing the following file failed:
  ‘model-based-annotations.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘nlmixr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggpolypath.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 16-21 (ggpolypath.Rmd) 
Error: processing vignette 'ggpolypath.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggpolypath.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘grammar-extensions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'ggpp'

The following object is masked from 'package:ggplot2':

    annotate


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 148-158 (grammar-extensions.Rmd) 
Error: processing vignette 'grammar-extensions.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘grammar-extensions.Rmd’

SUMMARY: processing the following file failed:
  ‘grammar-extensions.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘axes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 38-48 (axes.Rmd) 
Error: processing vignette 'axes.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘axes.Rmd’

--- re-building ‘colours.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 44-51 (colours.Rmd) 
Error: processing vignette 'colours.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘colours.Rmd’

--- re-building ‘ggprism.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 45-59 (ggprism.Rmd) 
Error: processing vignette 'ggprism.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggprism.Rmd’

--- re-building ‘pvalues.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 66-74 (pvalues.Rmd) 
Error: processing vignette 'pvalues.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘pvalues.Rmd’

--- re-building ‘themes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 53-63 (themes.Rmd) 
Error: processing vignette 'themes.Rmd' failed with diagnostics:
polygon edge not found
--- 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggpval.Rmd’ using knitr
Quitting from lines 60-65 (ggpval.Rmd) 
Error: processing vignette 'ggpval.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggpval.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘XbarR_HOTTO.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 46-54 (XbarR_HOTTO.Rmd) 
Error: processing vignette 'XbarR_HOTTO.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘XbarR_HOTTO.Rmd’

--- re-building ‘XmR_HOWTO.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 35-43 (XmR_HOWTO.Rmd) 
Error: processing vignette 'XmR_HOWTO.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘XmR_HOWTO.Rmd’

SUMMARY: processing the following files failed:
  ‘XbarR_HOTTO.Rmd’ ‘XmR_HOWTO.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Raster_geoms.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-30 (Raster_geoms.Rmd) 
Error: processing vignette 'Raster_geoms.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Raster_geoms.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   22. │     └─grid::pushViewport(vp, recording = FALSE)
   23. │       └─base::lapply(vps, push.vp, recording)
   24. │         ├─grid:::FUN(X[[i]], ...)
   25. │         └─grid:::push.vp.vpTree(X[[i]], ...)
   26. │           ├─grid:::push.vp(vp$parent, recording)
   27. │           └─grid:::push.vp.viewport(vp$parent, recording)
   28. │             └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   29. └─(function (x) ...
   30.   ├─grid::widthDetails(x)
   31.   └─grid:::widthDetails.text(x)
   32.     └─grid:::grid.Call(...)
  
  [ FAIL 9 | WARN 45 | SKIP 0 | PASS 52 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 76-91 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggsci.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 136-139 (ggsci.Rmd) 
Error: processing vignette 'ggsci.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggsci.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggseas.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 47-49 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggseas.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggside_aes_mapping.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 31-35 (ggside_aes_mapping.Rmd) 
Error: processing vignette 'ggside_aes_mapping.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggside_aes_mapping.Rmd’

--- re-building ‘ggside_basic_usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 36-44 (ggside_basic_usage.Rmd) 
Error: processing vignette 'ggside_basic_usage.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggside_basic_usage.Rmd’

SUMMARY: processing the following files failed:
  ‘ggside_aes_mapping.Rmd’ ‘ggside_basic_usage.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘coding_overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘coding_overview.Rmd’

--- re-building ‘ggsolvencyii.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 70-194 (ggsolvencyii.Rmd) 
Error: processing vignette 'ggsolvencyii.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggsolvencyii.Rmd’

--- re-building ‘plotdetails.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘plotdetails.Rmd’

--- re-building ‘showcase.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-176 (showcase.Rmd) 
Error: processing vignette 'showcase.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘showcase.Rmd’

SUMMARY: processing the following files failed:
  ‘ggsolvencyii.Rmd’ ‘showcase.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘userguide1-grammar.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

News at https://www.r4photobiology.info/
ggspectra: default axis labels updated
Quitting from lines 142-143 (userguide1-grammar.Rmd) 
Error: processing vignette 'userguide1-grammar.Rmd' failed with diagnostics:
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--- failed re-building ‘userguide1-grammar.Rmd’

--- re-building ‘userguide2-autoplot-methods.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-63 (userguide2-autoplot-methods.Rmd) 
Error: processing vignette 'userguide2-autoplot-methods.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘userguide2-autoplot-methods.Rmd’

--- re-building ‘userguide3-data-manip.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 86-90 (userguide3-data-manip.Rmd) 
Error: processing vignette 'userguide3-data-manip.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘userguide3-data-manip.Rmd’

SUMMARY: processing the following files failed:
  ‘userguide1-grammar.Rmd’ ‘userguide2-autoplot-methods.Rmd’
  ‘userguide3-data-manip.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘plotting_text.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'glue'

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

    collapse

Quitting from lines 30-58 (plotting_text.Rmd) 
Error: processing vignette 'plotting_text.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘plotting_text.Rmd’

--- re-building ‘theme_elements.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 27-34 (theme_elements.Rmd) 
Error: processing vignette 'theme_elements.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘theme_elements.Rmd’

SUMMARY: processing the following files failed:
  ‘plotting_text.Rmd’ ‘theme_elements.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/GGUM.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggvoronoi.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 35-48 (ggvoronoi.Rmd) 
Error: processing vignette 'ggvoronoi.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggvoronoi.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   18. │ ├─grid::makeContent(x)
   19. │ └─ggwordcloud:::makeContent.textwordcloudtree(x)
   20. │   └─base::lapply(...)
   21. │     └─ggwordcloud:::FUN(X[[i]], ...)
   22. │       └─grid::convertWidth(grobWidth(tg_inch), "inch", TRUE)
   23. │         └─grid::convertUnit(...)
   24. │           └─grid:::grid.Call(...)
   25. └─(function (x) ...
   26.   ├─grid::widthDetails(x)
   27.   └─grid:::widthDetails.text(x)
   28.     └─grid:::grid.Call(...)
  
  [ FAIL 22 | WARN 26 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggwordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 63-67 (ggwordcloud.Rmd) 
Error: processing vignette 'ggwordcloud.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ggwordcloud.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘colors.Rmd’ using knitr
Quitting from lines 27-35 (colors.Rmd) 
Error: processing vignette 'colors.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘colors.Rmd’

--- re-building ‘labels.Rmd’ using knitr
Quitting from lines 27-34 (labels.Rmd) 
Error: processing vignette 'labels.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘labels.Rmd’

--- re-building ‘legend.Rmd’ using knitr
Quitting from lines 27-33 (legend.Rmd) 
Error: processing vignette 'legend.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘legend.Rmd’

SUMMARY: processing the following files failed:
  ‘colors.Rmd’ ‘labels.Rmd’ ‘legend.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  y[1]: "2021-07-27"
  ── Failure (test-get_info_files.R:14:3): get_info works ────────────────────────
  as.character(as.Date(infos$last_modif)) not equal to setNames(today, "last").
  1/1 mismatches
  x[1]: "2021-07-26"
  y[1]: "2021-07-27"
  ── Failure (test-get_info_files.R:19:3): get_info works ────────────────────────
  as.character(as.Date(infos_not_in_repo$last_modif)) not equal to setNames(today, "last").
  1/1 mismatches
  x[1]: "2021-07-26"
  y[1]: "2021-07-27"
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 55 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'rtracklayer', 'GenomicRanges', 'BSgenome',
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is 106.9Mb
  sub-directories of 1Mb or more:
    libs  105.6Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
installed size is 56.2Mb
  sub-directories of 1Mb or more:
    libs  55.5Mb
Error(s) in re-building vignettes:
--- re-building ‘spatial-glms.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Rcpp

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 38-53 (spatial-glms.Rmd) 
Error: processing vignette 'spatial-glms.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘spatial-glms.Rmd’

SUMMARY: processing the following file failed:
  ‘spatial-glms.Rmd’

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

Package suggested but not available for checking: ‘edgeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 47.3Mb
  sub-directories of 1Mb or more:
    libs  46.4Mb
installed size is 74.4Mb
  sub-directories of 1Mb or more:
    libs           69.9Mb
    test_data       2.0Mb
    vignette_data   1.1Mb
Running ‘AAAtest-all.R’ [37s/38s]
Running the tests in ‘tests/AAAtest-all.R’ failed.
Last 13 lines of output:
  
  52. cov_struct_order (test-varstruc.R:98:5) - Reason: On CRAN
  
  53. zi (test-zi.R:12:3) - Reason: On CRAN
  
  54. zi beta and Gamma (test-zi.R:37:5) - Reason: On CRAN
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Failure (test-basics.R:121:3): Update Binomial ───────────────────────────
  `gm1` not equal to matchForm(gm1, gm1u).
  Component "sdr": Component "gradient.fixed": Mean relative difference: 2.287797e-08
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘predicts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: MASS
Loading required package: parallel
* installing *source* package ‘schlegel’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Warning: object ‘.Random.seed’ is created by more than one data call
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (schlegel)
Quitting from lines 158-166 (predicts.Rmd) 
Error: processing vignette 'predicts.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘predicts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘glmtrans-demo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loaded glmnet 4.1-2
Quitting from lines 169-170 (glmtrans-demo.Rmd) 
Error: processing vignette 'glmtrans-demo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘glmtrans-demo.Rmd’

SUMMARY: processing the following file failed:
  ‘glmtrans-demo.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/glmulti.Rcheck/00install.out’ for details.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using knitr
--- finished re-building ‘introduction.Rmd’

--- re-building ‘plots.Rmd’ using knitr
Quitting from lines 37-38 (plots.Rmd) 
Error: processing vignette 'plots.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘plots.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.1Mb
    libs   2.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/gMCP.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘Descriptives.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

--- finished re-building ‘Descriptives.Rmd’

--- re-building ‘Grid-based_flowcharts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-89 (Grid-based_flowcharts.Rmd) 
Error: processing vignette 'Grid-based_flowcharts.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Grid-based_flowcharts.Rmd’

--- re-building ‘Transition-class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Rcpp
Loading required package: htmlTable
Quitting from lines 88-92 (Transition-class.Rmd) 
Error: processing vignette 'Transition-class.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Transition-class.Rmd’

--- re-building ‘transitionPlot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Rcpp
Loading required package: htmlTable
Quitting from lines 92-94 (transitionPlot.Rmd) 
Error: processing vignette 'transitionPlot.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘transitionPlot.Rmd’

SUMMARY: processing the following files failed:
  ‘Grid-based_flowcharts.Rmd’ ‘Transition-class.Rmd’
  ‘transitionPlot.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Packages required but not available: 'SeqArray', 'SeqVarTools'

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

Package suggested but not available for checking: ‘WGCNA’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 154.5Mb
  sub-directories of 1Mb or more:
    libs  153.6Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
This is gplite version 0.12.0
Quitting from lines 44-53 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [22s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(gppm)
  Loading required package: Rcpp
  > 
  > test_check("gppm")
Error(s) in re-building vignettes:
  ...
--- re-building ‘gprofiler2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 257-259 (gprofiler2.Rmd) 
Error: processing vignette 'gprofiler2.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gprofiler2.Rmd’

SUMMARY: processing the following file failed:
  ‘gprofiler2.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MPG_algorithm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘MPG_algorithm.Rmd’

--- re-building ‘grainscape_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 172-184 (grainscape_vignette.Rmd) 
Error: processing vignette 'grainscape_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘grainscape_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘hexSticker’
Error(s) in re-building vignettes:
--- re-building ‘genetic_graph_2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 95-118 (genetic_graph_2.Rmd) 
Error: processing vignette 'genetic_graph_2.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘genetic_graph_2.Rmd’

--- re-building ‘graph_comparisons_4.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 108-114 (graph_comparisons_4.Rmd) 
Error: processing vignette 'graph_comparisons_4.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘graph_comparisons_4.Rmd’

--- re-building ‘input_data_processing_1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 332-338 (input_data_processing_1.Rmd) 
Error: processing vignette 'input_data_processing_1.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘input_data_processing_1.Rmd’

--- re-building ‘landscape_graph_3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 117-134 (landscape_graph_3.Rmd) 
Error: processing vignette 'landscape_graph_3.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘landscape_graph_3.Rmd’

SUMMARY: processing the following files failed:
  ‘genetic_graph_2.Rmd’ ‘graph_comparisons_4.Rmd’
  ‘input_data_processing_1.Rmd’ ‘landscape_graph_3.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 113-114 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cricket.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 83-90 (cricket.Rmd) 
Error: processing vignette 'cricket.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘cricket.Rmd’

--- re-building ‘gravitas_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 119-139 (gravitas_vignette.Rmd) 
Error: processing vignette 'gravitas_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gravitas_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘cricket.Rmd’ ‘gravitas_vignette.Rmd’

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

Package suggested but not available for checking: ‘RBGL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘GMM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 55-56 (GMM.Rmd) 
Error: processing vignette 'GMM.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘GMM.Rmd’

--- re-building ‘graph-clustering-with-sbm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 49-50 (graph-clustering-with-sbm.Rmd) 
Error: processing vignette 'graph-clustering-with-sbm.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘graph-clustering-with-sbm.Rmd’

SUMMARY: processing the following files failed:
  ‘GMM.Rmd’ ‘graph-clustering-with-sbm.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  core_minimise_epl.cpp:14:8: warning: 'random_shuffle<double *, int (&)(int)>' is deprecated [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/GreedyEPL.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/GreedyExperimentalDesignJARs.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/GreedyExperimentalDesign.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘printCrudeAndAdjustedModel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: forestplot
Loading required package: grid
Loading required package: magrittr
Loading required package: checkmate
Loading required package: Gmisc
Loading required package: Rcpp
Loading required package: htmlTable
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

--- finished re-building ‘printCrudeAndAdjustedModel.Rmd’

--- re-building ‘timeSplitter.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: forestplot
Loading required package: grid
Loading required package: checkmate
Loading required package: Gmisc
Loading required package: Rcpp
Loading required package: htmlTable
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 145-272 (timeSplitter.Rmd) 
Error: processing vignette 'timeSplitter.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘timeSplitter.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.5Mb
installed size is 34.4Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
Error(s) in re-building vignettes:
--- re-building ‘arrangeGrob.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-33 (arrangeGrob.rmd) 
Error: processing vignette 'arrangeGrob.rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘arrangeGrob.rmd’

--- re-building ‘gtable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: knitr
Loading required package: gridExtra
Loading required package: grid
Loading required package: gtable
Loading required package: ggplot2
Quitting from lines 52-55 (gtable.Rmd) 
Error: processing vignette 'gtable.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gtable.Rmd’

--- re-building ‘ngonGrob.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘ngonGrob.Rmd’

--- re-building ‘tableGrob.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-29 (tableGrob.Rmd) 
Error: processing vignette 'tableGrob.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘tableGrob.Rmd’

SUMMARY: processing the following files failed:
  ‘arrangeGrob.rmd’ ‘gtable.Rmd’ ‘tableGrob.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘grob_layout.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 35-53 (grob_layout.Rmd) 
Error: processing vignette 'grob_layout.Rmd' failed with diagnostics:
invalid 'cex' value
--- failed re-building ‘grob_layout.Rmd’

--- re-building ‘grob_matrix.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 45-52 (grob_matrix.Rmd) 
Error: processing vignette 'grob_matrix.Rmd' failed with diagnostics:
invalid 'cex' value
--- failed re-building ‘grob_matrix.Rmd’

--- re-building ‘grobblR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 49-58 (grobblR.Rmd) 
Error: processing vignette 'grobblR.Rmd' failed with diagnostics:
invalid 'cex' value
--- failed re-building ‘grobblR.Rmd’

SUMMARY: processing the following files failed:
  ‘grob_layout.Rmd’ ‘grob_matrix.Rmd’ ‘grobblR.Rmd’

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

Package suggested but not available for checking: ‘snplist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 63-64 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 22-34 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘profiling.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘interval’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   3.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘GuessCompx.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 60-62 (GuessCompx.Rmd) 
Error: processing vignette 'GuessCompx.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘GuessCompx.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gunsales.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 33-34 (gunsales.Rmd) 
Error: processing vignette 'gunsales.Rmd' failed with diagnostics:
Process terminated
--- failed re-building ‘gunsales.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   5.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gwqs-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
`geom_smooth()` using formula 'y ~ x'
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 58-87 (gwqs-vignette.Rmd) 
Error: processing vignette 'gwqs-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gwqs-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is 179.5Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    java  176.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   1.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 132-139 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘quickstart.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Basic_use.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hazus_demo.Rmd’ using knitr
Quitting from lines 109-119 (hazus_demo.Rmd) 
Error: processing vignette 'hazus_demo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘hazus_demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    extdata   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hchinamap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'https://czxb.github.io/br/chinadf.rda'
Content type 'application/octet-stream' length 3992 bytes
==================================================
downloaded 3992 bytes

Quitting from lines 50-58 (hchinamap.Rmd) 
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘hchinamap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/hdf5r.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘hdme.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loaded glmnet 4.1-2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 155-161 (hdme.Rmd) 
Error: processing vignette 'hdme.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘hdme.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdpGLM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 103-104 (hdpGLM.Rmd) 
Error: processing vignette 'hdpGLM.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘hdpGLM.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [30s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   15. │                       └─ggplot2::max_width(lapply(grobs, function(x) x$widths[2]))
   16. │                         ├─base::unlist(lapply(grobs, width_cm))
   17. │                         └─base::lapply(grobs, width_cm)
   18. │                           └─ggplot2:::FUN(X[[i]], ...)
   19. │                             └─grid::convertWidth(x, "cm", TRUE)
   20. │                               └─grid::convertUnit(...)
   21. │                                 └─grid:::grid.Call(...)
   22. └─(function (x) ...
   23.   ├─grid::widthDetails(x)
   24.   └─grid:::widthDetails.text(x)
   25.     └─grid:::grid.Call(...)
  
  [ FAIL 1 | WARN 19 | SKIP 0 | PASS 503 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/helloJavaWorld.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘hermiter.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'data.table'

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

    between, first, last

Quitting from lines 289-294 (hermiter.Rmd) 
Error: processing vignette 'hermiter.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘hermiter.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  23.6Mb
Package suggested but not available for checking: ‘marray’
Error(s) in re-building vignettes:
  ...
--- re-building ‘hhcartr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 342-343 (hhcartr.Rmd) 
Error: processing vignette 'hhcartr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘hhcartr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Packages required but not available: 'GenomicRanges', 'rtracklayer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘HierDpart.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-60 (HierDpart.Rmd) 
Error: processing vignette 'HierDpart.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘HierDpart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/HierO.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.9Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs       10.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Supersonic_Routes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 126-148 (Supersonic_Routes.Rmd) 
Error: processing vignette 'Supersonic_Routes.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Supersonic_Routes.Rmd’

--- re-building ‘Supersonic_Routes_in_depth.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 110-149 (Supersonic_Routes_in_depth.Rmd) 
Error: processing vignette 'Supersonic_Routes_in_depth.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Supersonic_Routes_in_depth.Rmd’

SUMMARY: processing the following files failed:
  ‘Supersonic_Routes.Rmd’ ‘Supersonic_Routes_in_depth.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Packages required but not available: 'InterpretMSSpectrum', 'Rdisop'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   6.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/hive.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘HiveR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 191-192 (HiveR.Rmd) 
Error: processing vignette 'HiveR.Rmd' failed with diagnostics:
invalid value specified for graphical parameter "mai"
--- failed re-building ‘HiveR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Error(s) in re-building vignettes:
--- re-building ‘allele-haplotype.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ dplyr   1.0.7
✔ tibble  3.1.3     ✔ stringr 1.4.0
✔ tidyr   1.1.3     ✔ forcats 0.5.1
✔ purrr   0.3.4     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
--- finished re-building ‘allele-haplotype.Rmd’

--- re-building ‘eplet-mm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.3     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   2.0.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 71-88 (eplet-mm.Rmd) 
Error: processing vignette 'eplet-mm.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘eplet-mm.Rmd’

SUMMARY: processing the following file failed:
  ‘eplet-mm.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.9Mb
Packages required but not available:
  'bamsignals', 'GenomicRanges', 'GenomicTools.fileHandler',
  'Rsamtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘horseshoe-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 53-68 (horseshoe-vignette.Rmd) 
Error: processing vignette 'horseshoe-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘horseshoe-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hpackedbubble.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘hpackedbubble.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘classstructure.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘classstructure.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 224-226 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘why_hrbrthemes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 36-51 (why_hrbrthemes.Rmd) 
Error: processing vignette 'why_hrbrthemes.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘why_hrbrthemes.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hsrecombi_workflow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 173-202 (hsrecombi_workflow.Rmd) 
Error: processing vignette 'hsrecombi_workflow.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘hsrecombi_workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 84.7Mb
  sub-directories of 1Mb or more:
    libs  84.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.3Mb
Package required but not available: ‘edgeR’

Package suggested but not available for checking: ‘HTSFilter’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.5Mb
installed size is 43.6Mb
  sub-directories of 1Mb or more:
    libs  43.3Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    doc    1.1Mb
    libs   6.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_hydroscoper.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 128-138 (intro_hydroscoper.Rmd) 
Error: processing vignette 'intro_hydroscoper.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro_hydroscoper.Rmd’

--- re-building ‘stations_with_data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-61 (stations_with_data.Rmd) 
Error: processing vignette 'stations_with_data.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘stations_with_data.Rmd’

SUMMARY: processing the following files failed:
  ‘intro_hydroscoper.Rmd’ ‘stations_with_data.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      2.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hydroTSM_Vignette-knitr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 107-119 (hydroTSM_Vignette-knitr.Rmd) 
Error: processing vignette 'hydroTSM_Vignette-knitr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘hydroTSM_Vignette-knitr.Rmd’

SUMMARY: processing the following file failed:
  ‘hydroTSM_Vignette-knitr.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Getting_started_with_the_R_package_hystReet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'lubridate'

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

    date, intersect, setdiff, union


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: httr
Loading required package: jsonlite
Quitting from lines 127-134 (Getting_started_with_the_R_package_hystReet.Rmd) 
Error: processing vignette 'Getting_started_with_the_R_package_hystReet.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Getting_started_with_the_R_package_hystReet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'BiocStyle', 'ComplexHeatmap'
Error(s) in re-building vignettes:
  ...
--- re-building ‘i2dash-extension.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 2-26 (i2dash-extension.Rmd) 
Error: processing vignette 'i2dash-extension.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘i2dash-extension.Rmd’

--- re-building ‘i2dash-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 2-26 (i2dash-intro.Rmd) 
Error: processing vignette 'i2dash-intro.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘i2dash-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitting_epicurves.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 38-45 (fitting_epicurves.Rmd) 
Error: processing vignette 'fitting_epicurves.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘fitting_epicurves.Rmd’

--- re-building ‘peak_estimation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘peak_estimation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette-IAbin.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 92-94 (vignette-IAbin.Rmd) 
Error: processing vignette 'vignette-IAbin.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘vignette-IAbin.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   6.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ibmsunburst.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘ibmsunburst.Rmd’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Package required but not available: ‘KEGGgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘LTRCtrees’
Package unavailable to check Rd xrefs: ‘LTRCtrees’
Packages required but not available: 'graphite', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.9Mb
Package required but not available: ‘hdf5r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Package required but not available: ‘Icens’

Packages suggested but not available for checking:
  'interval', 'mixAK', 'FHtest', 'runjags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘reference.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 159-160 (reference.Rmd) 
Error: processing vignette 'reference.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘reference.Rmd’

--- re-building ‘strategies.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 103-104 (strategies.Rmd) 
Error: processing vignette 'strategies.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘strategies.Rmd’

--- re-building ‘utilities.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘utilities.Rmd’

--- re-building ‘xoanda.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘xoanda.Rmd’

SUMMARY: processing the following files failed:
  ‘reference.Rmd’ ‘strategies.Rmd’

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

> ### Name: dist.simu.test
> ### Title: Cut-Off Values Using Simulations for the Detection of Extreme
> ###   ICS Distances
> ### Aliases: dist.simu.test
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> # For a real analysis use larger values for m and more cores if available
> 
> Z <- rmvnorm(1000, rep(0, 6))
> Z[1:20, 1] <- Z[1:20, 1] + 10
> A <- matrix(rnorm(36), ncol = 6)
> X <- tcrossprod(Z, A)
> 
> pairs(X)
> icsX <- ics2(X)
> 
> icsX.dist.1 <- ics.distances(icsX, index = 1)
> CutOff <- dist.simu.test(icsX, 1, m = 500, ncores = 1)
> 
> # check if outliers are above the cut-off value
> plot(icsX.dist.1, col = rep(2:1, c(20, 980)))
> abline(h = CutOff)
> 
> 
> library(REPPlab)
Loading required package: rJava
Loading required package: lattice
Loading required package: LDRTools
Error(s) in re-building vignettes:
  ...
--- re-building ‘cICS_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: polynom
Loading required package: ggplot2
Quitting from lines 47-51 (cICS_vignette.Rmd) 
Error: processing vignette 'cICS_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘cICS_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  35.1Mb
Packages suggested but not available for checking: 'ggtree', 'treeio'
Package required but not available: ‘mzR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Error(s) in re-building vignettes:
--- re-building ‘AGP_and_Episodes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-25 (AGP_and_Episodes.Rmd) 
Error: processing vignette 'AGP_and_Episodes.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘AGP_and_Episodes.Rmd’

--- re-building ‘iglu.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 275-277 (iglu.Rmd) 
Error: processing vignette 'iglu.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘iglu.Rmd’

--- re-building ‘lasagna_plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-26 (lasagna_plots.Rmd) 
Error: processing vignette 'lasagna_plots.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘lasagna_plots.Rmd’

--- re-building ‘metrics_list.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘metrics_list.Rmd’

SUMMARY: processing the following files failed:
  ‘AGP_and_Episodes.Rmd’ ‘iglu.Rmd’ ‘lasagna_plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IgorR)
  > 
  > test_check("IgorR")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-ibw.R:28:3): Processing of dates ──────────────────────────────
  .convertIgorDate(3444214517) not equivalent to as.POSIXct("2013-02-20 14:15:17").
  Mean relative difference: 3.966714e-06
  
  [ FAIL 1 | WARN 61 | SKIP 0 | PASS 35 ]
  Error: Test failures
  Execution halted
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   1.1Mb
    libs  20.0Mb
Package suggested but not available for checking: ‘EBImage’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package unavailable to check Rd xrefs: ‘EBImage’
Error(s) in re-building vignettes:
--- re-building ‘reading-and-writing-images.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Using basic display functionality.
  * For better display functionality, install the EBImage package.
  * To install `EBImage`:
    - Install `BiocManager` with `install.packages("BiocManager")`.
    - Then run `BiocManager::install("EBImage")`.
Quitting from lines 50-62 (reading-and-writing-images.Rmd) 
Error: processing vignette 'reading-and-writing-images.Rmd' failed with diagnostics:
figure margins too large
--- failed re-building ‘reading-and-writing-images.Rmd’

--- re-building ‘text-images.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘text-images.Rmd’

--- re-building ‘the-imagej-problem.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Reading Rlogo-banana-red_green.tif: an 8-bit, 155x200 pixel
image of unsigned integer type. Reading 2 channels and 2
frames . . .
 Done.
Using basic display functionality.
  * For better display functionality, install the EBImage package.
  * To install `EBImage`:
    - Install `BiocManager` with `install.packages("BiocManager")`.
    - Then run `BiocManager::install("EBImage")`.
Quitting from lines 53-66 (the-imagej-problem.Rmd) 
Error: processing vignette 'the-imagej-problem.Rmd' failed with diagnostics:
figure margins too large
--- failed re-building ‘the-imagej-problem.Rmd’

SUMMARY: processing the following files failed:
  ‘reading-and-writing-images.Rmd’ ‘the-imagej-problem.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘image.CornerDetectionF9-Ex.R’ failed
The error most likely occurred in:

> ### Name: image_detect_corners
> ### Title: Find Corners in Digital Images with FAST-9.
> ### Aliases: image_detect_corners
> 
> ### ** Examples
> 
> library(pixmap)
> imagelocation <- system.file("extdata", "chairs.pgm", package="image.CornerDetectionF9")
> image   <- read.pnm(file = imagelocation, cellres = 1)
Read 262144 items
> x       <- image@grey * 255
> corners <- image_detect_corners(x, 80)
> plot(image)
> points(corners$x, corners$y, col = "red", pch = 20, lwd = 0.5)
> 
> ##
> ## image_detect_corners expects a matrix as input
> ##  if you have a jpg/png/... convert it to pgm first or take the r/g/b channel
> library(magick)
Linking to ImageMagick 6.9.12.3
Enabled features: cairo, fontconfig, freetype, heic, lcms, pango, raw, rsvg, webp
Disabled features: fftw, ghostscript, x11
> x <- image_read(system.file("extdata", "hall.jpg", package="image.CornerDetectionF9"))
> x
  format width height colorspace matte filesize density
1   JPEG   450    565       Gray FALSE    17541   72x72
> image   <- image_data(x, channels = "Gray")
> image   <- as.integer(image, transpose = TRUE)
> image   <- drop(image)
> corners <- image_detect_corners(image, threshold = 80)
> 
> plt <- image_draw(x)
Fontconfig error: Cannot load default config file
Error in graphics::mtext(sprintf("help(\"%s\")", nameEx()), side = 4,  : 
  R: UnableToReadFont `helvetica' @ error/annotate.c/RenderFreetype/1396
Running examples in ‘image.CornerDetectionHarris-Ex.R’ failed
The error most likely occurred in:

> ### Name: image_harris
> ### Title: Find Corners using Harris Corner Detection
> ### Aliases: image_harris
> 
> ### ** Examples
> 
> library(magick)
Linking to ImageMagick 6.9.12.3
Enabled features: cairo, fontconfig, freetype, heic, lcms, pango, raw, rsvg, webp
Disabled features: fftw, ghostscript, x11
> path <- system.file(package = "image.CornerDetectionHarris", 
+                     "extdata", "building.png")
> x    <- image_read(path)
> pts  <- image_harris(x)
> pts
Harris Corner Detector
  found 251 corners
> 
> plt <- image_draw(x)
Fontconfig error: Cannot load default config file
Error in graphics::mtext(sprintf("help(\"%s\")", nameEx()), side = 4,  : 
  R: UnableToReadFont `helvetica' @ error/annotate.c/RenderFreetype/1396
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.1Mb
    libs         5.2Mb
Running examples in ‘image.dlib-Ex.R’ failed
The error most likely occurred in:

> ### Name: image_surf
> ### Title: Find SURF points in an image
> ### Aliases: image_surf
> 
> ### ** Examples
> 
> library(magick)
Linking to ImageMagick 6.9.12.3
Enabled features: cairo, fontconfig, freetype, heic, lcms, pango, raw, rsvg, webp
Disabled features: fftw, ghostscript, x11
> f <- system.file("extdata", "cruise_boat.png", package = "image.dlib")
> x <- image_read(f)
> x
  format width height colorspace matte filesize density
1    PNG   654    400       sRGB FALSE   273271   28x28
> surf_blobs <- image_data(x, channels = "rgb")
> surf_blobs <- as.integer(surf_blobs, transpose = FALSE)
> surf_blobs <- image_surf(surf_blobs, max_points = 10000, detection_threshold = 50)
> str(surf_blobs)
List of 8
 $ points       : num 150
 $ x            : num [1:150] 161 161 164 196 260 ...
 $ y            : num [1:150] 279 280 258 255 266 ...
 $ angle        : num [1:150] -3.09 3.14 2.39 2.12 -1.45 ...
 $ pyramid_scale: num [1:150] 3.67 3.8 2.09 2.23 2.24 ...
 $ score        : num [1:150] 948 884 631 545 491 ...
 $ laplacian    : num [1:150] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 ...
 $ surf         : num [1:150, 1:64] 0.00473 0.00974 -0.04304 -0.00386 0.01034 ...
> 
> library(magick)
> plt <- image_draw(x)
Fontconfig error: Cannot load default config file
Error in graphics::mtext(sprintf("help(\"%s\")", nameEx()), side = 4,  : 
  R: UnableToReadFont `helvetica' @ error/annotate.c/RenderFreetype/1396
Running examples in ‘image.libfacedetection-Ex.R’ failed
The error most likely occurred in:

> ### Name: image_detect_faces
> ### Title: Detect faces in images using the libfacedetection CNN
> ### Aliases: image_detect_faces
> 
> ### ** Examples
> 
> library(magick)
Linking to ImageMagick 6.9.12.3
Enabled features: cairo, fontconfig, freetype, heic, lcms, pango, raw, rsvg, webp
Disabled features: fftw, ghostscript, x11
> path <- system.file(package="image.libfacedetection", "images", "handshake.jpg")
> x <- image_read(path)
> x
  format width height colorspace matte filesize density
1   JPEG  1024    683       sRGB FALSE   168117   72x72
> faces <- image_detect_faces(x)
> faces
$nr
[1] 3

$detections
    x   y width height confidence landmark1_x landmark1_y landmark2_x
1 741 171    64     85         99         753         206         782
2 270 124    60     81         99         292         151         319
3 429 146    56     78         99         446         178         472
  landmark2_y landmark3_x landmark3_y landmark4_x landmark4_y landmark5_x
1         207         764         224         755         235         780
2         155         307         169         290         181         313
3         177         461         194         448         204         472
  landmark5_y
1         235
2         184
3         203

attr(,"class")
[1] "libfacedetection"
> plot(faces, x, border = "red", lwd = 7, col = "white", landmarks = TRUE)
Fontconfig error: Cannot load default config file
Error in graphics::mtext(sprintf("help(\"%s\")", nameEx()), side = 4,  : 
  R: UnableToReadFont `helvetica' @ error/annotate.c/RenderFreetype/1396
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     25.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘IMaGES.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in strheight(main, "inches", cex.main) :
  no font could be found for family "Arial"
Quitting from lines 119-131 (IMaGES.Rmd) 
Error: processing vignette 'IMaGES.Rmd' failed with diagnostics:
invalid value specified for graphical parameter "mai"
--- failed re-building ‘IMaGES.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs   12.4Mb
    share  10.2Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R  11.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘imbalance.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 70-75 (imbalance.Rmd) 
Error: processing vignette 'imbalance.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘imbalance.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Quitting from lines 79-83 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro.Rmd’

--- re-building ‘parallel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 47-50 (parallel.Rmd) 
Error: processing vignette 'parallel.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘parallel.Rmd’

SUMMARY: processing the following files failed:
  ‘intro.Rmd’ ‘parallel.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'clusterProfiler', 'GSEABase', 'GSVA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Cheat_Sheet_imputeTS.pdf.asis’ using asis
--- finished re-building ‘Cheat_Sheet_imputeTS.pdf.asis’

--- re-building ‘imputeTS-Time-Series-Missing-Value-Imputation-in-R.ltx’ using tex
--- finished re-building ‘imputeTS-Time-Series-Missing-Value-Imputation-in-R.ltx’

--- re-building ‘gallery_visualizations.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (gallery_visualizations.Rmd) 
Error: processing vignette 'gallery_visualizations.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘gallery_visualizations.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
Packages required but not available: 'siggenes', 'genefilter', 'RankProd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Error(s) in re-building vignettes:
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-63 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction.Rmd’

--- re-building ‘alternative_date_groupings.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘alternative_date_groupings.Rmd’

--- re-building ‘customizing_incidence_plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-60 (customizing_incidence_plots.Rmd) 
Error: processing vignette 'customizing_incidence_plots.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘customizing_incidence_plots.Rmd’

--- re-building ‘handling_incidence_objects.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building ‘handling_incidence_objects.Rmd’

SUMMARY: processing the following files failed:
  ‘Introduction.Rmd’ ‘customizing_incidence_plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘incidental-tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 85-86 (incidental-tutorial.Rmd) 
Error: processing vignette 'incidental-tutorial.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘incidental-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘incidental-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘incR_pipeline.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 116-125 (incR_pipeline.Rmd) 
Error: processing vignette 'incR_pipeline.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘incR_pipeline.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘EstimatingIncidence.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘EstimatingIncidence.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘SurveyDesign.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘SurveyDesign.Rmd’

--- re-building ‘TestCalibration.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 97-98 (TestCalibration.Rmd) 
Error: processing vignette 'TestCalibration.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘TestCalibration.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 253-255 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
In addition: There were 15 warnings (use warnings() to see them)
Execution halted
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
No path to the binary executable of X-13 specified.

You can set 'X13_PATH' manually if you intend to use your own
binaries. See ?seasonal for details.

Error in checkX13(fail = TRUE, fullcheck = FALSE, htmlcheck = FALSE) : 
  Process terminated
Calls: INFL.core_tf -> <Anonymous> -> checkX13
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Information-vignette.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 223-224 (Information-vignette.Rmd) 
Error: processing vignette 'Information-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Information-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/InSilicoVA.Rcheck/00install.out’ for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Packages required but not available:
  'GenomicRanges', 'GenomicAlignments', 'biomaRt', 'Rsamtools',
  'DESeq2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/InterfaceqPCR.Rcheck/00install.out’ for details.
installed size is 28.5Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
Package required but not available: ‘Rdisop’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intkriging-workflow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 116-121 (intkriging-workflow.Rmd) 
Error: processing vignette 'intkriging-workflow.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intkriging-workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘intkriging-workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.1Mb
Running examples in ‘ipeadatar-Ex.R’ failed
The error most likely occurred in:

> ### Name: available_subjects
> ### Title: List with available subjects
> ### Aliases: available_subjects
> 
> ### ** Examples
> 
> # Available subjects (in English)
> all_subjects <- available_subjects()
Warning: `mutate_()` was deprecated in dplyr 0.7.0.
Please use `mutate()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `arrange_()` was deprecated in dplyr 0.7.0.
Please use `arrange()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `select_()` was deprecated in dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error in open.connection(con, "rb") : HTTP error 502.
Calls: available_subjects ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘common_ipf_problems.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 165-166 (common_ipf_problems.Rmd) 
Error: processing vignette 'common_ipf_problems.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘common_ipf_problems.Rmd’

--- re-building ‘using_ipfr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 139-140 (using_ipfr.Rmd) 
Error: processing vignette 'using_ipfr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘using_ipfr.Rmd’

SUMMARY: processing the following files failed:
  ‘common_ipf_problems.Rmd’ ‘using_ipfr.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Running ‘test-all.R’ [1s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_ip_conversion.R:42:3): Error handlers for numeric to dotted-decimal work ──
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "255.255.255.255"
  y[1]: "0.0.0.0"
  Backtrace:
      █
   1. └─testthat::expect_that(result, equals("0.0.0.0")) test_ip_conversion.R:42:2
   2.   └─testthat:::condition(object)
   3.     └─testthat::expect_equal(x, expected, ..., expected.label = label)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 81 ]
  Error: Test failures
  Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Namespaces in Imports field not imported from:
  ‘coda’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘IRATER-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
sh: admb: command not found
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rectifiedI.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 33-42 (rectifiedI.Rmd) 
Error: processing vignette 'rectifiedI.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘rectifiedI.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘getting-started-with-irg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
ndvi                    package:irg                    R Documentation

_R_a_w _N_D_V_I _T_i_m_e _S_e_r_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     A data.table containing NDVI samples for ten points over ten years
     (2002-2012).

_F_o_r_m_a_t:

     A data.table with 2530 rows and 5 variables:

        • id - individual identifier

        • yr - year of sample

        • DayOfYear - julian day/day of year of sample

        • NDVI - sampled value

        • SummaryQA - Summary quality assessment value

     SummaryQA details:

        • 0 - Good data, use with confidence

        • 1 - Marginal data, useful but look at detailed QA for more
          information

        • 2 - Pixel covered with snow/ice

        • 3 - Pixel is cloudy

_E_x_a_m_p_l_e_s:

     # Load data.table
     library(data.table)
     
     # Read example data
     ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg"))
     

Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘getting-started-with-irg.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R  12.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘iriR_Vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘iriR_Vignette.Rmd’

--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 157-158 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Running examples in ‘ISEtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: analyseISE
> ### Title: Ion selective electrode characterisation and estimation of
> ###   sample concentrations
> ### Aliases: analyseISE
> 
> ### ** Examples
> 
> # Fast-running example with only 100 MCMC iterations for testing:
> data(LeadStdAdd)
> example2test = analyseISE(LeadStdAdd, Z = 2, temperature = 21, 
+   burnin=100, iters=200, chains=1, a.init=c(176, 146, -112), 
+   b.init=c(29, 30, 31), cstar.init=c(0.26, 0.27, 0.22), program="jags")
Warning in library(x, character.only = TRUE, logical.return = TRUE) :
  there is no package called ‘rjags’
[1] "The rjags package must be installed to use jags."
> print(example2test)
NULL
> summary(example2test)
Length  Class   Mode 
     0   NULL   NULL 
> plot(example2test, ylim = c(-7, -3), xlab = "ID (Sample)", 
+      ylab = expression(paste(log[10], " ", Pb^{paste("2","+",sep="")} )))
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'xlim' values
Calls: plot -> plot.default -> localWindow -> plot.window
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/ISM.Rcheck/00install.out’ for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘isocat.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-83 (isocat.Rmd) 
Error: processing vignette 'isocat.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘isocat.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Package required but not available: ‘ConsensusClusterPlus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: pkgmaker
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
# NOTE - CRAN check detected: limiting maximum number of cores [2/8]
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 2/2 | CRAN check
Quitting from lines 45-47 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ivmte.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 675-703 (ivmte.Rmd) 
Error: processing vignette 'ivmte.Rmd' failed with diagnostics:
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--- failed re-building ‘ivmte.Rmd’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/jdx.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 11.2Mb
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    libs  10.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   7.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘joineRmeta.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 227-229 (joineRmeta.Rmd) 
Error: processing vignette 'joineRmeta.Rmd' failed with diagnostics:
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--- failed re-building ‘joineRmeta.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.9Mb
Package which this enhances but not available for checking: ‘MRCE’
Package suggested but not available for checking: ‘PSCBS’
Package unavailable to check Rd xrefs: ‘PSCBS’
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 82-83 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘boral’
installed size is  6.4Mb
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    doc    1.5Mb
    libs   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘jskm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 35-45 (jskm.Rmd) 
Error: processing vignette 'jskm.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘jskm.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/jsr223.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [4s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   3.   └─jstor:::.f(.x[[i]], ...)
   4.     └─testthat::expect_identical(...) test-zip.R:48:4
  ── Failure (test-zip.R:51:3): importing from zip works ─────────────────────────
  read_csv(file.path("testfiles", expected_file)) not identical to read_csv(file.path(test_dir, expected_file)).
  Objects equal but not identical
  Backtrace:
      █
   1. ├─expected_files %>% purrr::map(test_expected_zip) test-zip.R:51:2
   2. └─purrr::map(., test_expected_zip)
   3.   └─jstor:::.f(.x[[i]], ...)
   4.     └─testthat::expect_identical(...) test-zip.R:48:4
  
  [ FAIL 11 | WARN 1 | SKIP 4 | PASS 242 ]
  Error: Test failures
  Execution halted
installed size is  5.3Mb
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    doc    2.0Mb
    libs   3.2Mb
Error(s) in re-building vignettes:
--- re-building ‘diagnostics-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 57-64 (diagnostics-vignette.Rmd) 
Error: processing vignette 'diagnostics-vignette.Rmd' failed with diagnostics:
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--- failed re-building ‘diagnostics-vignette.Rmd’

--- re-building ‘exploratory-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 286-293 (exploratory-vignette.Rmd) 
Error: processing vignette 'exploratory-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘exploratory-vignette.Rmd’

--- re-building ‘model-test-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘model-test-vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘diagnostics-vignette.Rmd’ ‘exploratory-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘awesome_table_in_html.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 635-638 (awesome_table_in_html.Rmd) 
Error: processing vignette 'awesome_table_in_html.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘awesome_table_in_html.Rmd’

--- re-building ‘awesome_table_in_pdf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘awesome_table_in_pdf.Rmd’

--- re-building ‘best_practice_for_newline_in_latex_table.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘best_practice_for_newline_in_latex_table.Rmd’

--- re-building ‘legacy_features.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘legacy_features.Rmd’

--- re-building ‘use_kable_in_shiny.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘use_kable_in_shiny.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘Choquet.integral-methods.R’ [0s/0s]
  Running ‘Mobius-methods.R’ [0s/1s]
  Running ‘Mobius.capacity-class.R’ [0s/0s]
  Running ‘Mobius.card.set.func-class.R’ [1s/1s]
  Running ‘Mobius.game-class.R’ [0s/1s]
  Running ‘Mobius.set.func-class.R’ [0s/1s]
  Running ‘Shapley.value-methods.R’ [0s/1s]
  Running ‘capacity-class.R’ [0s/1s]
  Running ‘card.capacity-class.R’ [0s/1s]
  Running ‘card.game-class.R’ [0s/1s]
  Running ‘card.set.func-class.R’ [0s/1s]
  Running ‘conjugate-methods.R’ [0s/1s]
  Running ‘entropy-methods.R’ [0s/1s]
  Running ‘entropy.capa.ident.R’ [0s/1s]
  Running ‘heuristic.ls.capa.ident.R’ [1s/1s]
  Running ‘interaction.indices-methods.R’ [0s/1s]
  Running ‘is.cardinal-methods.R’ [0s/1s]
  Running ‘is.kadditive-methods.R’ [0s/1s]
  Running ‘is.monotone-methods.R’ [0s/1s]
  Running ‘k.truncate.Mobius-methods.R’ [0s/1s]
  Running ‘least.squares.capa.ident.R’ [1s/1s]
  Running ‘lin.prog.capa.ident.R’ [0s/1s]
  Running ‘ls.sorting.treatment.R’ [0s/1s]
Running the tests in ‘tests/ls.sorting.treatment.R’ failed.
Last 13 lines of output:
  >         # Aiap <- c(1,1,2,2)
  >          Aiap <- NULL
  >         
  > 	print("*** Starting the calculations")
  [1] "*** Starting the calculations"
  > 	## search for a capacity which satisfies the constraints
  > 	lsc <- ls.sorting.capa.ident(n ,k, P, cl.proto, d,
  +                                    A.Shapley.preorder = Asp,
  +                                    A.Shapley.interval = Asi,
  +                                    A.interaction.preorder = Aip,
  +                                    A.interaction.interval = Aii,
  +                                    A.inter.additive.partition = Aiap)
  Error in ls.sorting.capa.ident(n, k, P, cl.proto, d, A.Shapley.preorder = Asp,  : 
    not enough classes
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kayadata.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-66 (kayadata.Rmd) 
Error: processing vignette 'kayadata.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘kayadata.Rmd’

--- re-building ‘policy_analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 88-90 (policy_analysis.Rmd) 
Error: processing vignette 'policy_analysis.Rmd' failed with diagnostics:
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--- failed re-building ‘policy_analysis.Rmd’

SUMMARY: processing the following files failed:
  ‘kayadata.Rmd’ ‘policy_analysis.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  20.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘kdtools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘kdtools.Rmd’

--- re-building ‘methods.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 85-98 (methods.Rmd) 
Error: processing vignette 'methods.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘methods.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
File ‘KernelICA/libs/KernelICA.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
    Objects: ‘KernelICAProblem.o’, ‘RcppExports.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘org.Hs.eg.db’
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Packages required but not available: 'Rsamtools', 'rtracklayer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘fitdistrplus’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-kindisperse.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 107-111 (using-kindisperse.Rmd) 
Error: processing vignette 'using-kindisperse.Rmd' failed with diagnostics:
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--- failed re-building ‘using-kindisperse.Rmd’

SUMMARY: processing the following file failed:
  ‘using-kindisperse.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pedigree.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: kinship2
Loading required package: Matrix
Loading required package: quadprog
Quitting from lines 70-76 (pedigree.Rmd) 
Error: processing vignette 'pedigree.Rmd' failed with diagnostics:
Labels leave no room for the graph, reduce cex
--- failed re-building ‘pedigree.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘klsh.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: stringdist
Loading required package: plyr
Quitting from lines 163-179 (klsh.Rmd) 
Error: processing vignette 'klsh.Rmd' failed with diagnostics:
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--- failed re-building ‘klsh.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/kmcudaR.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘kmedoid.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 939-940 (kmedoid.Rmd) 
Error: processing vignette 'kmedoid.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘kmedoid.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘KMunicate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-63 (KMunicate.Rmd) 
Error: processing vignette 'KMunicate.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘KMunicate.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘data_language_engine_vignette.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required namespace: gpg
Quitting from lines 134-135 (data_language_engine_vignette.Rmd) 
Error: processing vignette 'data_language_engine_vignette.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘data_language_engine_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘run-all.R’ [4s/6s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testit)
  > test_pkg("knitr")
  Error from withRestarts(stop(cond), retry_loadNamespace = function() NULL) 
  Error in loadNamespace(x) : there is no package called 'tibble'
  Calls: test_pkg ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  In addition: There were 37 warnings (use warnings() to see them)
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-konfound.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 68-69 (introduction-to-konfound.Rmd) 
Error: processing vignette 'introduction-to-konfound.Rmd' failed with diagnostics:
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--- failed re-building ‘introduction-to-konfound.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kraljic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 145-152 (kraljic.Rmd) 
Error: processing vignette 'kraljic.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘kraljic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘shiny-app.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘shiny-app.Rmd’

--- re-building ‘tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 41-48 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  13.1Mb
Running examples in ‘L1mstate-Ex.R’ failed
The error most likely occurred in:

> ### Name: cumhaz.l1mstate
> ### Title: Compute subject-specific transition hazard rates
> ### Aliases: cumhaz.l1mstate
> ### Keywords: multi-state models regularization
> 
> ### ** Examples
> 
> #### EBMT data
> data(ebmt4)
> 
> x1 <- ifelse(ebmt4$match=="gender mismatch", 1, 0)
> x2 <- ifelse(ebmt4$proph=="yes", 1, 0)
> x3 <- ifelse(ebmt4$year=="1990-1994", 1, 0)
> x4 <- ifelse(ebmt4$year=="1995-1998", 1, 0)
> x5 <- ifelse(ebmt4$agecl=="20-40", 1, 0)
> x6 <- ifelse(ebmt4$agecl==">40", 1, 0)
> dt <- data.frame(ebmt4[,1:11],x1,x2,x3,x4,x5,x6)
> col_names <- c("x1", "x2", "x3", "x4", "x5", "x6")
> tmat <- transMat(x = list(c(2,3,5,6),c(4,5,6),c(4,5,6),c(5,6),c(),c()),  
+                  names = c("Tx", "Rec", "AE", "Rec+AE", "Rel", "Death"))
> dat <- msprep(data = dt, trans = tmat, time = c(NA, "rec", "ae", 
+                 "recae","rel", "srv"),status = c(NA, "rec.s", "ae.s", 
+                 "recae.s","rel.s", "srv.s"), keep = col_names)
> # select the first 450 lines for a sake of illustration
> dat <- dat[1:450,]
> out <- cv.l1mstateR(dat, nlambda = 100, nfolds = 10)
Error in if (nzMax != 0) { : argument is of length zero
Calls: cv.l1mstateR
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘labsimplex.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 66-69 (labsimplex.Rmd) 
Error: processing vignette 'labsimplex.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘labsimplex.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
Packages required but not available: 'GOstats', 'GOSemSim'

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

> ### Name: spc,SpatialPixelsDataFrame-method
> ### Title: Generate Principal Components using SpatialPixelsDataFrame
> ###   object
> ### Aliases: spc,SpatialPixelsDataFrame-method spc
> 
> ### ** Examples
> 
> library(plotKML)
Error in library(plotKML) : there is no package called ‘plotKML’
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs             3.3Mb
    shiny-landsepi   1.3Mb
Error(s) in re-building vignettes:
--- re-building ‘lans2r-calculate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 102-109 (lans2r-calculate.Rmd) 
Error: processing vignette 'lans2r-calculate.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘lans2r-calculate.Rmd’

--- re-building ‘lans2r-hmr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 33-39 (lans2r-hmr.Rmd) 
Error: processing vignette 'lans2r-hmr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘lans2r-hmr.Rmd’

--- re-building ‘lans2r.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 92-103 (lans2r.Rmd) 
Error: processing vignette 'lans2r.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘lans2r.Rmd’

SUMMARY: processing the following files failed:
  ‘lans2r-calculate.Rmd’ ‘lans2r-hmr.Rmd’ ‘lans2r.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    help   1.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/lar.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘mixAK’
Package unavailable to check Rd xrefs: ‘mixAK’
Error(s) in re-building vignettes:
--- re-building ‘custom.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-63 (custom.Rmd) 
Error: processing vignette 'custom.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘custom.Rmd’

--- re-building ‘demo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-51 (demo.Rmd) 
Error: processing vignette 'demo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘demo.Rmd’

--- re-building ‘validation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘validation.Rmd’

SUMMARY: processing the following files failed:
  ‘custom.Rmd’ ‘demo.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'gof', 'lava.tobit', 'lme4'
Error(s) in re-building vignettes:
  ...
--- re-building ‘LBSPR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 233-234 (LBSPR.Rmd) 
Error: processing vignette 'LBSPR.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘LBSPR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.0Mb
    libs   1.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘topics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 84-85 (topics.Rmd) 
Error: processing vignette 'topics.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘topics.Rmd’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘VariantAnnotation’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ldsr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 86-105 (ldsr.Rmd) 
Error: processing vignette 'ldsr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ldsr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘usage-leaflet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: sp
Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
  Discarded ellps WGS 84 in Proj4 definition: +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs +type=crs
Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
  Discarded datum World Geodetic System 1984 in Proj4 definition
Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
  Discarded ellps WGS 84 in Proj4 definition: +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs +type=crs
Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
  Discarded datum World Geodetic System 1984 in Proj4 definition
Quitting from lines 32-38 (usage-leaflet.Rmd) 
Error: processing vignette 'usage-leaflet.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘usage-leaflet.Rmd’

--- re-building ‘usage-leafletProxy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘usage-leafletProxy.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  21.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/leidenAlg.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   4.2Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  11.0Mb
installed size is 93.9Mb
  sub-directories of 1Mb or more:
    libs  92.7Mb
Running ‘testthat.R’ [6s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  lo\$format_event\(tevent\) does not match "ERROR .*2018-11-02 .*:19:33.*\\.* foo bar".
  Actual value: "ERROR \[2018-11-03 05:19:33\.930\] foo bar"
  Backtrace:
      █
   1. └─testthat::expect_match(lo$format_event(tevent), "ERROR .*2018-11-02 .*:19:33.*\\.* foo bar") test_Layout.R:25:2
   2.   └─testthat:::expect_match_(...)
  ── Failure (test_Layout.R:29:3): LayoutFormat works as expected ────────────────
  lo$format_event(tevent) not identical to "[2018-11-02]".
  1/1 mismatches
  x[1]: "[2018-11-03]"
  y[1]: "[2018-11-02]"
  
  [ FAIL 2 | WARN 2 | SKIP 2 | PASS 555 ]
  Error: Test failures
  Execution halted
installed size is 38.8Mb
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    libs  38.6Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    extdata   1.1Mb
    libs      9.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘summary.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 129-130 (summary.Rmd) 
Error: processing vignette 'summary.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘summary.Rmd’

--- re-building ‘vignette_viz.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 32-33 (vignette_viz.Rmd) 
Error: processing vignette 'vignette_viz.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vignette_viz.Rmd’

SUMMARY: processing the following files failed:
  ‘summary.Rmd’ ‘vignette_viz.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.8Mb
installed size is 54.8Mb
  sub-directories of 1Mb or more:
    libs  54.2Mb
Packages required but not available: 'M3C', 'pathifier', 'pathview', 'RCy3'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Understanding_lime.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 167-168 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Understanding_lime.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘geometry_parameter_space.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 65-78 (geometry_parameter_space.Rmd) 
Error: processing vignette 'geometry_parameter_space.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘geometry_parameter_space.Rmd’

--- re-building ‘liminal.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 65-70 (liminal.Rmd) 
Error: processing vignette 'liminal.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘liminal.Rmd’

SUMMARY: processing the following files failed:
  ‘geometry_parameter_space.Rmd’ ‘liminal.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘linear.tools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 157-162 (linear.tools.Rmd) 
Error: processing vignette 'linear.tools.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘linear.tools.Rmd’

SUMMARY: processing the following file failed:
  ‘linear.tools.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > set.seed(1)
  > X <- as.data.frame(matrix(runif(5500), ncol = 11, nrow = 500))
  > X2 <- X
  > X2$V1 <- as.factor(as.character(X2$V1 > 0.5))
  > local <- sample_locally(data = X,
  +                          explained_instance = X[3, ],
  +                          explained_var = "V1",
  +                          size = 50)
  > local1 <- add_predictions(local, "regr.svm", X)
  > if(require('RWeka')) {
  +   local_explained <- fit_explanation(local1, "regr.lm")
  +   local_explained2 <- fit_explanation(local1, "regr.svm", kernel = identity_kernel)
  + }
  Loading required package: RWeka
Error(s) in re-building vignettes:
--- re-building ‘wine_quality.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ParamHelpers
Warning message: 'mlr' is in 'maintenance-only' mode since July 2019.
Future development will only happen in 'mlr3'
(<https://mlr3.mlr-org.com>). Due to the focus on 'mlr3' there might be
uncaught bugs meanwhile in {mlr} - please consider switching.
Welcome to live v1.5.13. Live is a part of DALEXverse. Find out more at https://github.com/pbiecek/DALEX.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'e1071'

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

    impute

Loading required package: RWeka
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/llama.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/LLM.Rcheck/00install.out’ for details.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.0Mb
    libs      23.0Mb
    testdata   1.3Mb
installed size is 68.0Mb
  sub-directories of 1Mb or more:
    libs  67.0Mb
Package required but not available: ‘genefilter’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/loa.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘localfdr-intro-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 137-138 (localfdr-intro-vignette.Rmd) 
Error: processing vignette 'localfdr-intro-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘localfdr-intro-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘logisticPCA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 112-114 (logisticPCA.Rmd) 
Error: processing vignette 'logisticPCA.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘logisticPCA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘logitnorm.Rmd’ using knitr
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 45-76 (logitnorm.Rmd) 
Error: processing vignette 'logitnorm.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘logitnorm.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘lolog-ergm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 69-75 (lolog-ergm.Rmd) 
Error: processing vignette 'lolog-ergm.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘lolog-ergm.Rmd’

--- re-building ‘lolog-introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 406-409 (lolog-introduction.Rmd) 
Error: processing vignette 'lolog-introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘lolog-introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘lolog-ergm.Rmd’ ‘lolog-introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘RDRToolbox’
Package suggested but not available for checking: ‘biomaRt’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  • empty test (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-coding.genes.R:15:3): (code run outside of `test_that()`) ───────
  Error: there is no package called 'biomaRt'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-coding.genes.R:15:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 211 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

biomaRt is not installed, only using genes from NCBI (CCDS)
Skipping biomaRt (is mart valid?: FALSE -- is biomaRt installed?: FALSE)
Coding genes from biomaRt: 0
   Coding genes from CCDS: 19029
            added by CCDS: 19029
-------------------------------
    total number of genes: 19029
Quitting from lines 129-144 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lotri-motivation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 119-147 (lotri-motivation.Rmd) 
Error: processing vignette 'lotri-motivation.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘lotri-motivation.Rmd’

SUMMARY: processing the following file failed:
  ‘lotri-motivation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.2Mb
Package required but not available: ‘GeneticsPed’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 53.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  50.9Mb
Error(s) in re-building vignettes:
--- re-building ‘factor-analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 100-101 (factor-analysis.Rmd) 
Error: processing vignette 'factor-analysis.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘factor-analysis.Rmd’

--- re-building ‘missing-data-analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘missing-data-analysis.Rmd’

--- re-building ‘multi-group-analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘multi-group-analysis.Rmd’

--- re-building ‘regression-analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (regression-analysis.Rmd) 
Error: processing vignette 'regression-analysis.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘regression-analysis.Rmd’

--- re-building ‘structural-equation-modeling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘structural-equation-modeling.Rmd’

SUMMARY: processing the following files failed:
  ‘factor-analysis.Rmd’ ‘regression-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘custom-models.Rmd’ using knitr
Loading required package: mcmc
Loading required package: MHadaptive
Loading required package: MASS
Loading required package: numDeriv
--- finished re-building ‘custom-models.Rmd’

--- re-building ‘example-plots.Rmd’ using knitr
Loading required package: mcmc
Loading required package: MHadaptive
Loading required package: MASS
Loading required package: numDeriv
Quitting from lines 24-59 (example-plots.Rmd) 
Error: processing vignette 'example-plots.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘example-plots.Rmd’

SUMMARY: processing the following file failed:
  ‘example-plots.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
      date, intersect, setdiff, union
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Fixm ymd_hms OSz parsing (2)
  • On CRAN (6)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-round.R:347:3): round_date does not round dates that are already on a boundary ──
  round_date(as.Date("2012-09-27"), "day") not equal to as.Date("2012-09-27").
  Mean relative difference: 6.40574e-05
  
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 2678 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lucid_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: lucid
Loading required package: lattice
Quitting from lines 141-166 (lucid_examples.Rmd) 
Error: processing vignette 'lucid_examples.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘lucid_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   4.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   1.2Mb
    libs   2.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   4.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘accuracy_indices.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘accuracy_indices.Rmd’

--- re-building ‘working_with_models.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Matrix
Quitting from lines 43-45 (working_with_models.Rmd) 
Error: processing vignette 'working_with_models.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘working_with_models.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 122.1Mb
  sub-directories of 1Mb or more:
    libs  122.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘lwqs-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 67-117 (lwqs-vignette.Rmd) 
Error: processing vignette 'lwqs-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘lwqs-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'GenomicRanges', 'GenomicAlignments', 'GenomicFeatures', 'Rsamtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘macleish.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: etl
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Loading required package: mgcv
Loading required package: nlme

Attaching package: 'nlme'

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

    collapse

This is mgcv 1.8-36. For overview type 'help("mgcv-package")'.
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
Quitting from lines 97-111 (macleish.Rmd) 
Error: processing vignette 'macleish.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘macleish.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  36.1Mb
Packages required but not available:
  'TCGAbiolinks', 'maftools', 'ComplexHeatmap', 'GenomicRanges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘udunits2’
Packages required but not available: 'SeqArray', 'SeqVarTools', 'GMMAT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 142.4Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    libs  135.4Mb
Running examples in ‘magick-Ex.R’ failed
The error most likely occurred in:

> ### Name: autoviewer
> ### Title: RStudio Graphics AutoViewer
> ### Aliases: autoviewer autoviewer_enable autoviewer_disable
> 
> ### ** Examples
> 
> # Only has effect in RStudio (or other GUI with a viewer):
> autoviewer_enable()
> 
> img <- magick::image_graph()
> plot(1)
Error in graphics::mtext(sprintf("help(\"%s\")", nameEx()), side = 4,  : 
  R: UnableToReadFont `helvetica' @ error/annotate.c/RenderFreetype/1396
Error in axis(side = side, at = at, labels = labels, ...) : 
  R: UnableToReadFont `helvetica' @ error/annotate.c/RenderFreetype/1396
Calls: plot ... plot.default -> localAxis -> Axis -> Axis.default -> axis
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Linking to librsvg 2.50.3
Fontconfig error: Cannot load default config file
Quitting from lines 227-236 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
R: NonconformingDrawingPrimitiveDefinition `text' @ error/draw.c/RenderMVGContent/4405
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'dittoSeq', 'BiocStyle'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Download.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 18-31 (Download.Rmd) 
Error: processing vignette 'Download.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘Download.Rmd’

--- re-building ‘Upload.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 18-31 (Upload.Rmd) 
Error: processing vignette 'Upload.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘Upload.Rmd’

SUMMARY: processing the following files failed:
  ‘Download.Rmd’ ‘Upload.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'RGtk2', 'gWidgets2RGtk2', 'ssize'

Packages suggested but not available for checking:
  'convert', 'marray', 'GEOquery', 'GEOmetadb', 'RBGL', 'WGCNA',
  'KEGGgraph', 'cairoDevice', 'pdInfoBuilder', 'lumi', 'oligo',
  'genefilter', 'simpleaffy', 'beadarray', 'GOstats', 'GO.db',
  'globaltest', 'Category'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/mailR.Rcheck/00install.out’ for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.3Mb
    libs   5.8Mb
Error(s) in re-building vignettes:
--- re-building ‘latin_square.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 86-87 (latin_square.Rmd) 
Error: processing vignette 'latin_square.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘latin_square.Rmd’

--- re-building ‘make_prior.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 141-145 (make_prior.Rmd) 
Error: processing vignette 'make_prior.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘make_prior.Rmd’

--- re-building ‘neonatal_mortality.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘neonatal_mortality.Rmd’

--- re-building ‘wheat_breeding.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 90-91 (wheat_breeding.Rmd) 
Error: processing vignette 'wheat_breeding.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘wheat_breeding.Rmd’

SUMMARY: processing the following files failed:
  ‘latin_square.Rmd’ ‘make_prior.Rmd’ ‘wheat_breeding.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   1.1Mb
    libs      2.3Mb
Error(s) in re-building vignettes:
--- re-building ‘MALDIrppa_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: MALDIquant

This is MALDIquant version 1.19.3
Quantitative Analysis of Mass Spectrometry Data
 See '?MALDIquant' for more information about this package.

Loading required package: signal

Attaching package: 'signal'

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

    filter, poly

Loading required package: robustbase
Loading required package: lattice
Quitting from lines 82-85 (MALDIrppa_vignette.Rmd) 
Error: processing vignette 'MALDIrppa_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MALDIrppa_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/mallet.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   22. │     └─grid::pushViewport(vp, recording = FALSE)
   23. │       └─base::lapply(vps, push.vp, recording)
   24. │         ├─grid:::FUN(X[[i]], ...)
   25. │         └─grid:::push.vp.vpTree(X[[i]], ...)
   26. │           ├─grid:::push.vp(vp$parent, recording)
   27. │           └─grid:::push.vp.viewport(vp$parent, recording)
   28. │             └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   29. └─(function (x) ...
   30.   ├─grid::widthDetails(x)
   31.   └─grid:::widthDetails.text(x)
   32.     └─grid:::grid.Call(...)
  
  [ FAIL 1 | WARN 45 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘manymodelr_vignette.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 327-333 (manymodelr_vignette.rmd) 
Error: processing vignette 'manymodelr_vignette.rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘manymodelr_vignette.rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs         19.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mapmisc.Rnw’ using knitr
Loading required package: sp
Loading required package: raster
map images will be cached in  /Volumes/Temp/tmp/RtmpMwTZif/mapmiscCache
Quitting from lines 456-475 (mapmisc.Rnw) 
Error: processing vignette 'mapmisc.Rnw' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘mapmisc.Rnw’

--- re-building ‘north.Rmd’ using docco_linear
Quitting from lines 85-95 (north.Rmd) 
Error: processing vignette 'north.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘north.Rmd’

pandoc --self-contained --to=html5 --css=http://diseasemapping.r-forge.r-project.org/webpage.css --output=north.html north.md	
make: pandoc: No such file or directory
make: *** [north.html] Error 1
Error in tools:::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.1/mapmisc.Rcheck/vign_test/mapmisc",  : 
  running 'make' failed
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   3.1Mb
    libs   4.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 114-119 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘markedVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: lme4
Loading required package: Matrix
Loading required package: parallel
This is marked 1.2.6

255 capture histories collapsed into 53
Computing initial parameter estimates

Starting optimization for 2 parameters...

Elapsed time in minutes:  0.0042 

255 capture histories collapsed into 53
Computing initial parameter estimates

Starting optimization for 3 parameters...

Elapsed time in minutes:  0.0026 

Computing initial parameter estimates

Starting optimization for 4 parameters...

Elapsed time in minutes:  0.0024 

Computing initial parameter estimates

Starting optimization for 7 parameters...

Elapsed time in minutes:  0.0029 

Computing initial parameter estimates

Starting optimization for 8 parameters...

Elapsed time in minutes:  0.0027 

255 capture histories collapsed into 53
Computing initial parameter estimates

Starting optimization for 3 parameters...

Elapsed time in minutes:  0.0028 

Computing initial parameter estimates

Starting optimization for 4 parameters...

Elapsed time in minutes:  0.0025 

Computing initial parameter estimates

Starting optimization for 7 parameters...

Elapsed time in minutes:  0.0026 

Computing initial parameter estimates

Starting optimization for 8 parameters...

Elapsed time in minutes:  0.003 

Quitting from lines 339-347 (markedVignette.Rmd) 
Error: processing vignette 'markedVignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘markedVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      12.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MarketMatching-Vignette.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 114-115 (MarketMatching-Vignette.Rmd) 
Error: processing vignette 'MarketMatching-Vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MarketMatching-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘MarketMatching-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_marketer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 49-63 (introduction_to_marketer.Rmd) 
Error: processing vignette 'introduction_to_marketer.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction_to_marketer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘estimaterates.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 83-87 (estimaterates.Rmd) 
Error: processing vignette 'estimaterates.Rmd' failed with diagnostics:
invalid symbol parameter
--- failed re-building ‘estimaterates.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Packages required but not available: 'GO.db', 'GOstats', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 195-199 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/matchingMarkets.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘policy_evaluation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 40-60 (policy_evaluation.Rmd) 
Error: processing vignette 'policy_evaluation.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘policy_evaluation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  12.7Mb
Errors in running code in vignettes:
when running code in ‘sparseModels.Rnw’
  ...
> png("sparseModels-X-sparse-image.png", width = 6, 
+     height = 3, units = "in", res = 150)

> print(image(t(smm), aspect = 1/3, lwd = 0, col.regions = "red"))
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"

  When sourcing ‘sparseModels.R’:
Error: polygon edge not found
Execution halted

  ‘Comparisons.Rnw’ using ‘UTF-8’... [8s/8s] OK
  ‘Design-issues.Rnw’ using ‘UTF-8’... [1s/1s] OK
  ‘Intro2Matrix.Rnw’ using ‘UTF-8’... [1s/1s] OK
  ‘Introduction.Rnw’ using ‘UTF-8’... [0s/0s] OK
  ‘sparseModels.Rnw’ using ‘UTF-8’... failed
Error(s) in re-building vignettes:
--- re-building ‘Comparisons.Rnw’ using Sweave
--- finished re-building ‘Comparisons.Rnw’

--- re-building ‘Design-issues.Rnw’ using Sweave
--- finished re-building ‘Design-issues.Rnw’

--- re-building ‘Intro2Matrix.Rnw’ using Sweave
<sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient
<sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient
--- finished re-building ‘Intro2Matrix.Rnw’

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

--- re-building ‘sparseModels.Rnw’ using Sweave
   [[ suppressing 20 column names ‘1’, ‘2’, ‘3’ ... ]]
   [[ suppressing 24 column names ‘1’, ‘2’, ‘3’ ... ]]
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"

Error: processing vignette 'sparseModels.Rnw' failed with diagnostics:
 chunk 15 (label = X-sparse-image-fake) 
Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  : 
  polygon edge not found

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Running ‘allocArray.R’ [0s/0s]
  Running ‘allocMatrix.R’ [0s/0s]
  Running ‘allocVector.R’ [0s/0s]
  Running ‘anyMissing.R’ [0s/0s]
  Running ‘anyMissing_subset.R’ [0s/0s]
  Running ‘benchmark.R’ [3s/3s]
Running the tests in ‘tests/benchmark.R’ failed.
Last 13 lines of output:
  + rm(list = "pkgs")
  + 
  + }
  Loading required namespace: base64enc
  Loading required namespace: ggplot2
  Loading required namespace: knitr
  Loading required namespace: microbenchmark
  Loading required namespace: R.devices
  Loading required namespace: R.rsp
  integer: unsorted
  Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  : 
    polygon edge not found
  Calls: <Anonymous> ... <Anonymous> -> widthDetails -> widthDetails.text -> grid.Call
  In addition: There were 30 warnings (use warnings() to see them)
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘matsindf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 385-397 (matsindf.Rmd) 
Error: processing vignette 'matsindf.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘matsindf.Rmd’

--- re-building ‘midf_apply_primer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘midf_apply_primer.Rmd’

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

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

> ### Name: mazeHTML
> ### Title: Generate Elithorn Maze
> ### Aliases: mazeHTML
> 
> ### ** Examples
> 
> 
> rank <- 3
> satPercent <- 0.5
> 
> #Grid must be same as rank
> grid <- gridThreeUp
> 
> #Folder to save html/
> #setwd("~/desktop")
> #filePath<- getwd()
> 
> #Generate item
> mazeHTML(rank,satPercent,seed=5,grid = grid,wd=NULL,
+ background="#7abcff",boxBackground="#66CDAA", fontColour="white ",
+ Timer=TRUE, concerto="C5")
HTML file is saved in default working directory.
no font could be found for family "Arial"Error in value[[3L]](cond) : 
 Stop: Rank and grid coordinates are not the same. (e.g, rank = 3, grid = gridThreeUp) 
Calls: mazeHTML ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package suggested but not available for checking: ‘emojifont’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(mazing)
  > 
  > test_check("mazing")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-mazing.R:79:5): advanced maze/matrix manipulation works ───────
  mean(m) == mean(m2) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘inspiration.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Quitting from lines 123-130 (inspiration.Rmd) 
Error: processing vignette 'inspiration.Rmd' failed with diagnostics:
could not find function "emoji"
--- failed re-building ‘inspiration.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_mbbefd.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: fitdistrplus
Loading required package: MASS
Loading required package: survival
Loading required package: alabama
Loading required package: numDeriv
Loading required package: Rcpp
Package:  mbbefd
Version:  0.8.10
Date:     2021-06-08 07:40:02 UTC
BugReport: https://github.com/spedygiorgio/mbbefd/issues


Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 75-94 (Introduction_to_mbbefd.Rmd) 
Error: processing vignette 'Introduction_to_mbbefd.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction_to_mbbefd.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘kangar00’
Package unavailable to check Rd xrefs: ‘kangar00’
Running ‘testthat.R’ [10s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure (test_auditor_fitters.R:107:3): SubPopFitter iterates through all columns ──
  Check on out[[1]] is not TRUE
  
  `actual` is a character vector ('Element 1 is not >= 0.2')
  `expected` is a logical vector (TRUE)
  Element 1 is not >= 0.2
  Backtrace:
      █
   1. └─checkmate::expect_number(out[[1]], lower = 0.2, upper = 0.2) test_auditor_fitters.R:107:2
   2.   └─checkmate::makeExpectation(x, res, info, label)
   3.     └─testthat::expect_true(...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 129 ]
  Error: Test failures
  Execution halted
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  14.6Mb
Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

> fitBernoulli <- mcemGLMM(fixed = Mate ~ 0 + Cross, 
+     random = list(~0 + Female, ~0 + Male), data = salamander, 
+     family = "bernoulli", vcD .... [TRUNCATED] 

Execution halted

... incomplete output.  Crash?

  ‘mcemGLM-vignette.Rnw’... failed to complete the test
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
Packages required but not available: 'gRbase', 'abn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘diagnostic-pkgs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 107-117 (diagnostic-pkgs.Rmd) 
Error: processing vignette 'diagnostic-pkgs.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘diagnostic-pkgs.Rmd’

--- re-building ‘faq.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: coda
--- finished re-building ‘faq.Rmd’

SUMMARY: processing the following file failed:
  ‘diagnostic-pkgs.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 44.7Mb
  sub-directories of 1Mb or more:
    libs  43.6Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MCPModGeneral-Vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 54-60 (MCPModGeneral-Vignette.Rmd) 
Error: processing vignette 'MCPModGeneral-Vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MCPModGeneral-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘MCPModGeneral-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mcprofile.Rmd’ using knitr
Loading required package: ggplot2
Quitting from lines 111-119 (mcprofile.Rmd) 
Error: processing vignette 'mcprofile.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mcprofile.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Package which this enhances but not available for checking: ‘JointAI’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_and_usage_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-79 (Intro_and_usage_examples.Rmd) 
Error: processing vignette 'Intro_and_usage_examples.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Intro_and_usage_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mxr_basic_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 225-262 (mxr_basic_vignette.Rmd) 
Error: processing vignette 'mxr_basic_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mxr_basic_vignette.Rmd’

--- re-building ‘mxr_tapering_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘mxr_tapering_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 44.1Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  39.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-60 (advanced.Rmd) 
Error: processing vignette 'advanced.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘advanced.Rmd’

--- re-building ‘medicalrisk.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘medicalrisk.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cost-report-analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Quitting from lines 164-189 (cost-report-analysis.Rmd) 
Error: processing vignette 'cost-report-analysis.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘cost-report-analysis.Rmd’

--- re-building ‘provider_of_service_naming.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘provider_of_service_naming.Rmd’

SUMMARY: processing the following file failed:
  ‘cost-report-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘MEGENA_pipeline_10062016.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Quitting from lines 120-128 (MEGENA_pipeline_10062016.Rmd) 
Error: processing vignette 'MEGENA_pipeline_10062016.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MEGENA_pipeline_10062016.Rmd’

SUMMARY: processing the following file failed:
  ‘MEGENA_pipeline_10062016.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mekko-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 58-60 (mekko-vignette.Rmd) 
Error: processing vignette 'mekko-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mekko-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette_MR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 338-340 (Vignette_MR.Rmd) 
Error: processing vignette 'Vignette_MR.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Vignette_MR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  20.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   6.8Mb
installed size is 117.0Mb
  sub-directories of 1Mb or more:
    libs  116.3Mb
Packages required but not available: 'mixOmics', 'pcaMethods', 'ropls'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'phyloseq', 'biomformat'
Running ‘testthat.R’ [9s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("metacoder")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test--parsers_and_writers.R:202:3): Converting to phyloseq ───────────
  Error: there is no package called 'phyloseq'
  Backtrace:
      █
   1. └─base::library(phyloseq) test--parsers_and_writers.R:202:2
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 535 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'ChemmineR', 'Rdisop'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   1.8Mb
Error(s) in re-building vignettes:
--- re-building ‘dominance.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 80-83 (dominance.Rmd) 
Error: processing vignette 'dominance.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘dominance.Rmd’

--- re-building ‘heterogeneity.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 70-71 (heterogeneity.Rmd) 
Error: processing vignette 'heterogeneity.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘heterogeneity.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: nlme
This is mgcv 1.8-36. For overview type 'help("mgcv-package")'.
Quitting from lines 98-99 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

--- re-building ‘multivariate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 57-59 (multivariate.Rmd) 
Error: processing vignette 'multivariate.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘multivariate.Rmd’

SUMMARY: processing the following files failed:
  ‘dominance.Rmd’ ‘heterogeneity.Rmd’ ‘introduction.Rmd’
  ‘multivariate.Rmd’

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

Packages suggested but not available for checking: 'BiocStyle', 'snplist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘dataset-batch-processing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 31-41 (dataset-batch-processing.Rmd) 
Error: processing vignette 'dataset-batch-processing.Rmd' failed with diagnostics:
there is no package called 'udunits2'
--- failed re-building ‘dataset-batch-processing.Rmd’

--- re-building ‘dataset-single.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘dataset-single.Rmd’

--- re-building ‘package-download.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘package-download.Rmd’

--- re-building ‘reading-raster.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘reading-raster.Rmd’

SUMMARY: processing the following file failed:
  ‘dataset-batch-processing.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'metagenomeSeq', 'DESeq2', 'edgeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GEOquery', 'org.Hs.eg.db', 'annaffy', 'hgu133plus2.db',
  'hgu133a.db', 'hgu95av2.db'
Error(s) in re-building vignettes:
  ...
--- re-building ‘metan_start.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
|=========================================================|
| Multi-Environment Trial Analysis (metan) v1.15.0        |
| Author: Tiago Olivoto                                   |
| Type 'citation('metan')' to know how to cite metan      |
| Type 'vignette('metan_start')' for a short tutorial     |
| Visit 'https://bit.ly/pkgmetan' for a complete tutorial |
|=========================================================|
No issues detected while inspecting data.
Quitting from lines 74-75 (metan_start.Rmd) 
Error: processing vignette 'metan_start.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘metan_start.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘how_to_use_crosshairs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-51 (how_to_use_crosshairs.Rmd) 
Error: processing vignette 'how_to_use_crosshairs.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘how_to_use_crosshairs.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using-metapower.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-52 (Using-metapower.Rmd) 
Error: processing vignette 'Using-metapower.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Using-metapower.Rmd’

SUMMARY: processing the following file failed:
  ‘Using-metapower.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 79-80 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 132.5Mb
  sub-directories of 1Mb or more:
    libs  132.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaStan_BNHM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 43-69 (MetaStan_BNHM.Rmd) 
Error: processing vignette 'MetaStan_BNHM.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MetaStan_BNHM.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘metawho.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 116-118 (metawho.Rmd) 
Error: processing vignette 'metawho.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘metawho.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   4.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   3.1Mb
Running ‘testthat.R’ [15s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(metR)
  > # library(vdiffr)
  > 
  > test_check("metR")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (22)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (???): df was read correctly ────────────────────────────────────────
  Value hashes to cf6967a47f, not 7a56064fc1
  
  [ FAIL 1 | WARN 0 | SKIP 22 | PASS 167 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Visualization-tools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 51-54 (Visualization-tools.Rmd) 
Error: processing vignette 'Visualization-tools.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Visualization-tools.Rmd’

--- re-building ‘Working-with-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 46-51 (Working-with-data.Rmd) 
Error: processing vignette 'Working-with-data.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Working-with-data.Rmd’

SUMMARY: processing the following files failed:
  ‘Visualization-tools.Rmd’ ‘Working-with-data.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    5.4Mb
    libs  25.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mFLICA_demo.Rmd’ using knitr
Quitting from lines 15-19 (mFLICA_demo.Rmd) 
Error: processing vignette 'mFLICA_demo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mFLICA_demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Discriminability.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-58 (Discriminability.Rmd) 
Error: processing vignette 'Discriminability.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Discriminability.Rmd’

--- re-building ‘MGC.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 72-73 (MGC.Rmd) 
Error: processing vignette 'MGC.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MGC.Rmd’

--- re-building ‘class_simulations.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: mgc
Loading required package: ggplot2
Quitting from lines 40-42 (class_simulations.Rmd) 
Error: processing vignette 'class_simulations.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘class_simulations.Rmd’

--- re-building ‘dep_simulations.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: mgc
Loading required package: ggplot2
Quitting from lines 64-69 (dep_simulations.Rmd) 
Error: processing vignette 'dep_simulations.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘dep_simulations.Rmd’

SUMMARY: processing the following files failed:
  ‘Discriminability.Rmd’ ‘MGC.Rmd’ ‘class_simulations.Rmd’
  ‘dep_simulations.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘mgcviz.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-36. For overview type 'help("mgcv-package")'.
Loading required package: qgam
Loading required package: ggplot2
Registered S3 method overwritten by 'mgcViz':
  method from  
  +.gg   GGally

Attaching package: 'mgcViz'

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

    qqline, qqnorm, qqplot

Quitting from lines 66-70 (mgcviz.rmd) 
Error: processing vignette 'mgcviz.rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mgcviz.rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Safe-Censoring.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Safe-Censoring.Rmd’

sh: line 1: 33824 Trace/BPT trap: 5       '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpYIt3Ru/file83f044c6675' 2>&1 < '/Volumes/Temp/tmp/RtmpYIt3Ru/file83f033da8d87'
--- re-building ‘Safe-Substitution.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
SUMMARY: processing the following file failed:
  ‘Safe-Substitution.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  22.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  10.1Mb
Error(s) in re-building vignettes:
--- re-building ‘miceFast-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'mice'

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

    filter

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

    cbind, rbind

Loading required package: carData

Attaching package: 'dplyr'

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

    recode

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'data.table'

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

    between, first, last

Quitting from lines 83-84 (miceFast-intro.Rmd) 
Error: processing vignette 'miceFast-intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘miceFast-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘haven’
Packages required but not available:
  'phyloseq', 'DESeq2', 'dada2', 'SummarizedExperiment', 'DECIPHER',
  'edgeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Errors in running code in vignettes:
when running code in ‘Introduction_Guide.Rnw’
  ...
5 AK      1    1       4      15    0         1    0
6 AK      1    1       4      17    0         1    0

> mmplot(stat.data = edPov, map.data = statePolys, panel.types = c("labels", 
+     "dot", "dot", "map"), panel.data = list("state", "pov", "ed", 
+   .... [TRUNCATED] 

  When sourcing ‘Introduction_Guide.R’:
Error: polygon edge not found
Execution halted

  ‘Introduction_Guide.Rnw’... failed
Error(s) in re-building vignettes:
--- re-building ‘Introduction_Guide.Rnw’ using Sweave
Loading required package: maptools
Loading required package: sp
Checking rgeos availability: TRUE
Loading required package: RColorBrewer
Loading required package: rgdal
rgdal: version: 1.5-23, (SVN revision 1121)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.2.3, released 2021/04/27
Path to GDAL shared files: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/rgdal/gdal
GDAL binary built with GEOS: TRUE 
Loaded PROJ runtime: Rel. 7.2.1, January 1st, 2021, [PJ_VERSION: 721]
Path to PROJ shared files: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.4-5
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
Overwritten PROJ_LIB was /Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/rgdal/proj

Error: processing vignette 'Introduction_Guide.Rnw' failed with diagnostics:
 chunk 5 (label = fig1) 
Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  : 
  polygon edge not found

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘microsamplingDesign.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Rcpp
Quitting from lines 387-392 (microsamplingDesign.Rmd) 
Error: processing vignette 'microsamplingDesign.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘microsamplingDesign.Rmd’

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

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

Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19',
  'BSgenome.Mmusculus.UCSC.mm10'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  tprocess.cc:70:9: warning: 'swapcontext' is deprecated: first deprecated in macOS 10.6 - No longer supported [-Wdeprecated-declarations]
  tprocess.cc:89:9: warning: 'swapcontext' is deprecated: first deprecated in macOS 10.6 - No longer supported [-Wdeprecated-declarations]
  tprocess.cc:148:9: warning: 'getcontext' is deprecated: first deprecated in macOS 10.6 - No longer supported [-Wdeprecated-declarations]
  tprocess.cc:157:5: warning: 'makecontext' is deprecated: first deprecated in macOS 10.6 - No longer supported [-Wdeprecated-declarations]
  tprocess.cc:159:9: warning: 'swapcontext' is deprecated: first deprecated in macOS 10.6 - No longer supported [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/microsimulation.Rcheck/00install.out’ for details.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    lib    7.9Mb
    libs   4.0Mb
Package suggested but not available for checking: ‘gWidgets2RGtk2’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/mind.Rcheck/00install.out’ for details.
Packages required but not available: 'showtextdb', 'showtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘mi_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 61-64 (mi_vignette.Rmd) 
Error: processing vignette 'mi_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mi_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 140.8Mb
  sub-directories of 1Mb or more:
    libs  140.1Mb
Packages required but not available: 'globaltest', 'GlobalAncova'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.5Mb
Package required but not available: ‘R2jags’

Packages suggested but not available for checking: 'mixAK', 'BRugs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Generating-missing-values.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 72-74 (Generating-missing-values.Rmd) 
Error: processing vignette 'Generating-missing-values.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Generating-missing-values.Rmd’

SUMMARY: processing the following file failed:
  ‘Generating-missing-values.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mistral-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 252-255 (mistral-vignette.Rmd) 
Error: processing vignette 'mistral-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mistral-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  33.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    libs   1.8Mb
Error(s) in re-building vignettes:
--- re-building ‘BasicGenetics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘BasicGenetics.Rmd’

--- re-building ‘DistributionBuildingNComparison.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-63 (DistributionBuildingNComparison.Rmd) 
Error: processing vignette 'DistributionBuildingNComparison.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘DistributionBuildingNComparison.Rmd’

--- re-building ‘HypothesisTest.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-65 (HypothesisTest.Rmd) 
Error: processing vignette 'HypothesisTest.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘HypothesisTest.Rmd’

SUMMARY: processing the following files failed:
  ‘DistributionBuildingNComparison.Rmd’ ‘HypothesisTest.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 29-40 (basic.Rmd) 
Error: processing vignette 'basic.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘basic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: INTENT mismatch in argument 'b' between (1) and (2)
  Warning: INTENT mismatch in argument 'a' between (1) and (2)
  Warning: Shape mismatch in argument 'yvec' between (1) and (2)
  Warning: INTENT mismatch in argument 'icen' between (1) and (2)
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/mixor.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘mizer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 147-148 (mizer.Rmd) 
Error: processing vignette 'mizer.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mizer.Rmd’

--- re-building ‘model_description.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Note: Using f0, h, lambda, kappa and the predation kernel to calculate gamma.
Quitting from lines 52-55 (model_description.Rmd) 
Error: processing vignette 'model_description.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘model_description.Rmd’

SUMMARY: processing the following files failed:
  ‘mizer.Rmd’ ‘model_description.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MKinfer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 303-323 (MKinfer.Rmd) 
Error: processing vignette 'MKinfer.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MKinfer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘genefilter’
Error(s) in re-building vignettes:
  ...
--- re-building ‘MKpower.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 176-183 (MKpower.Rmd) 
Error: processing vignette 'MKpower.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MKpower.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/mleap.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘mlergm_tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ergm
Loading required package: network

'network' 1.17.1 (2021-06-12), part of the Statnet Project
* 'news(package="network")' for changes since last version
* 'citation("network")' for citation information
* 'https://statnet.org' for help, support, and other information


'ergm' 4.0.1 (2021-06-20), part of the Statnet Project
* 'news(package="ergm")' for changes since last version
* 'citation("ergm")' for citation information
* 'https://statnet.org' for help, support, and other information

'ergm' 4 is a major update that introduces some backwards-incompatible
changes. Please type 'news(package="ergm")' for a list of major
changes.

Quitting from lines 147-148 (mlergm_tutorial.Rmd) 
Error: processing vignette 'mlergm_tutorial.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mlergm_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 74-81 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MLID.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 48-104 (MLID.Rmd) 
Error: processing vignette 'MLID.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MLID.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'minfi', 'GEOquery', 'IlluminaHumanMethylation450kmanifest'
Running examples in ‘MLMOI-Ex.R’ failed
The error most likely occurred in:

> ### Name: moimerge
> ### Title: Merges two molecular datasets.
> ### Aliases: moimerge
> 
> ### ** Examples
> 
> #The datasets 'testDatamerge1.xlsx' and 'testDatamerge1.xlsx' are already in standard format:
> 
> infile1 <- system.file("extdata", "testDatamerge1.xlsx", package = "MLMOI")
> infile2 <- system.file("extdata", "testDatamerge2.xlsx", package = "MLMOI")
> outfile <- moimerge(infile1, infile2, nummtd1 = 1, nummtd2 = 2, keepmtd = TRUE)
Error(s) in re-building vignettes:
  ...
--- re-building ‘StandardAmbiguityCodes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘StandardAmbiguityCodes.Rmd’

--- re-building ‘dataimportcheck-list.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘dataimportcheck-list.Rmd’

sh: line 1: 51588 Trace/BPT trap: 5       '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpU7kTcS/filec93fd84f993' 2>&1 < '/Volumes/Temp/tmp/RtmpU7kTcS/filec93f151d28d4'
--- re-building ‘examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- re-building ‘moimport-arguments.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘moimport-arguments.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 411.1Mb
  sub-directories of 1Mb or more:
    libs  410.7Mb
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (requireNamespace("testthat", quietly = TRUE)) {
  +   library(checkmate)
  +   library(testthat)
  +   library(mlr3)
  +   library(mlr3cluster)
  + 
  +   test_check("mlr3cluster")
  + }
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(checkmate)
  > # library(mlr3oml)
  > 
  > test_check("mlr3oml")
  Loading required package: mlr3oml
Error(s) in re-building vignettes:
  ...
--- re-building ‘mlr3spatiotempcv.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘mlr3spatiotempcv.Rmd’

--- re-building ‘spatiotemp-viz.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 90-164 (spatiotemp-viz.Rmd) 
Error: processing vignette 'spatiotemp-viz.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘spatiotemp-viz.Rmd’

SUMMARY: processing the following file failed:
  ‘spatiotemp-viz.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘run-core.R’ [0s/0s]
  Running ‘run-cpo.R’ [6s/4s]
Running the tests in ‘tests/run-cpo.R’ failed.
Last 13 lines of output:
    1. └─testthat::test_check("mlrCPO", filter = "^cpo_")
    2.   └─testthat::test_dir(...)
    3.     └─testthat:::test_files(...)
    4.       └─testthat:::test_files(...)
    5.         ├─testthat::with_reporter(...)
    6.         │ ├─base::withRestarts(...)
    7.         │ │ └─base:::withOneRestart(expr, restarts[[1L]])
    8.         │ │   └─base:::doWithOneRestart(return(expr), restart)
    9.         │ └─base::force(code)
   10.         └─testthat:::parallel_event_loop_chunky(queue, reporters)
   11.           └─queue$poll(Inf)
   12.             └─base::lapply(...)
   13.               └─testthat:::FUN(X[[i]], ...)
   14.                 └─private$handle_error(msg, i)
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mlrMBO.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 63-67 (mlrMBO.Rmd) 
Error: processing vignette 'mlrMBO.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mlrMBO.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 76-80 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 40.2Mb
  sub-directories of 1Mb or more:
    libs  39.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MLZ.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 54-55 (MLZ.Rmd) 
Error: processing vignette 'MLZ.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MLZ.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Cluster-Analysis.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-95 (Cluster-Analysis.rmd) 
Error: processing vignette 'Cluster-Analysis.rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Cluster-Analysis.rmd’

SUMMARY: processing the following file failed:
  ‘Cluster-Analysis.rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ALL’
Running examples in ‘MMDvariance-Ex.R’ failed
The error most likely occurred in:

> ### Name: gsMMD.v
> ### Title: Gene selection based on variances by using a mixture of marginal
> ###   distributions
> ### Aliases: gsMMD.v
> ### Keywords: classif
> 
> ### ** Examples
> 
>       t1 = proc.time()
>       library(ALL)
Error in library(ALL) : there is no package called ‘ALL’
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Classification-as-typical-and-deviant.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 39-42 (Classification-as-typical-and-deviant.Rmd) 
Error: processing vignette 'Classification-as-typical-and-deviant.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Classification-as-typical-and-deviant.Rmd’

--- re-building ‘Extreme-case.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Extreme-case.Rmd’

--- re-building ‘Most-typical-and-most-deviant.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Most-typical-and-most-deviant.Rmd’

--- re-building ‘Pathway-case.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 41-42 (Pathway-case.Rmd) 
Error: processing vignette 'Pathway-case.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Pathway-case.Rmd’

SUMMARY: processing the following files failed:
  ‘Classification-as-typical-and-deviant.Rmd’ ‘Pathway-case.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘OVA_Predictions_For_MNL.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 152-163 (OVA_Predictions_For_MNL.Rmd) 
Error: processing vignette 'OVA_Predictions_For_MNL.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘OVA_Predictions_For_MNL.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘modcmfitrOverview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 304-389 (modcmfitrOverview.Rmd) 
Error: processing vignette 'modcmfitrOverview.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘modcmfitrOverview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘modelplotr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 423-424 (modelplotr.Rmd) 
Error: processing vignette 'modelplotr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘modelplotr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  length(wc$record) not equal to length(unique(iris$Species)).
  1/1 mismatches
  [1] 0 - 3 == -3
  ── Failure (test-wordcloud.R:249:5): it plots iris from a model object with three parameters ──
  length(wc$record) not equal to length(unique(iris$Species)).
  1/1 mismatches
  [1] 0 - 3 == -3
  ── Failure (test-wordcloud.R:263:5): it plots iris from a model object with four parameters ──
  length(wc$record) not equal to length(unique(iris$Species)).
  1/1 mismatches
  [1] 0 - 3 == -3
  
  [ FAIL 30 | WARN 182 | SKIP 0 | PASS 32 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘modistools-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 155-163 (modistools-vignette.Rmd) 
Error: processing vignette 'modistools-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘modistools-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      3.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    libs   5.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MoMPCA.Rmd’ using knitr
Quitting from lines 77-79 (MoMPCA.Rmd) 
Error: processing vignette 'MoMPCA.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MoMPCA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.6Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   8.5Mb
Error(s) in re-building vignettes:
--- re-building ‘mortAAR_vignette-1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 131-132 (mortAAR_vignette-1.Rmd) 
Error: processing vignette 'mortAAR_vignette-1.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mortAAR_vignette-1.Rmd’

--- re-building ‘mortAAR_vignette_extended.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 146-148 (mortAAR_vignette_extended.Rmd) 
Error: processing vignette 'mortAAR_vignette_extended.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mortAAR_vignette_extended.Rmd’

--- re-building ‘mortAAR_vignette_lt_correction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 28-31 (mortAAR_vignette_lt_correction.Rmd) 
Error: processing vignette 'mortAAR_vignette_lt_correction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mortAAR_vignette_lt_correction.Rmd’

--- re-building ‘mortAAR_vignette_reproduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in get_engine(options$engine) :
  Unknown language engine 'oxcal' (must be registered via knit_engines$set()).
--- finished re-building ‘mortAAR_vignette_reproduction.Rmd’

SUMMARY: processing the following files failed:
  ‘mortAAR_vignette-1.Rmd’ ‘mortAAR_vignette_extended.Rmd’
  ‘mortAAR_vignette_lt_correction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘international-mortality-tables-overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 67-69 (international-mortality-tables-overview.Rmd) 
Error: processing vignette 'international-mortality-tables-overview.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘international-mortality-tables-overview.Rmd’

--- re-building ‘using-the-mortalityTables-package.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Quitting from lines 136-145 (using-the-mortalityTables-package.Rmd) 
Error: processing vignette 'using-the-mortalityTables-package.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘using-the-mortalityTables-package.Rmd’

SUMMARY: processing the following files failed:
  ‘international-mortality-tables-overview.Rmd’
  ‘using-the-mortalityTables-package.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Calculus_with_R.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 111-112 (Calculus_with_R.Rmd) 
Error: processing vignette 'Calculus_with_R.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Calculus_with_R.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 66-68 (Basics.Rmd) 
Error: processing vignette 'Basics.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Basics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Resampling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 182-183 (Resampling.Rmd) 
Error: processing vignette 'Resampling.Rmd' failed with diagnostics:
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--- failed re-building ‘Resampling.Rmd’

--- re-building ‘mosaic-resources.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘mosaic-resources.Rmd’

--- re-building ‘MinimalRgg.Rnw’ using knitr
Loading required package: mosaic
Registered S3 method overwritten by 'mosaic':
  method                           from   
  fortify.SpatialPolygonsDataFrame ggplot2

The 'mosaic' package masks several functions from core packages in order to add 
additional features.  The original behavior of these functions should not be affected by this.

Attaching package: 'mosaic'

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

    count, do, tally

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

    mean

The following object is masked from 'package:ggplot2':

    stat

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

    IQR, binom.test, cor, cor.test, cov, fivenum, median, prop.test,
    quantile, sd, t.test, var

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

    max, mean, min, prod, range, sample, sum

Loading required package: parallel
Using parallel package.
  * Set seed with set.rseed().
  * Disable this message with options(`mosaic:parallelMessage` = FALSE)

Using parallel package.
  * Set seed with set.rseed().
  * Disable this message with options(`mosaic:parallelMessage` = FALSE)

--- finished re-building ‘MinimalRgg.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘demo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 391-402 (demo.Rmd) 
Error: processing vignette 'demo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘demo.Rmd’

--- re-building ‘multifidelity.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 203-214 (multifidelity.Rmd) 
Error: processing vignette 'multifidelity.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘multifidelity.Rmd’

SUMMARY: processing the following files failed:
  ‘demo.Rmd’ ‘multifidelity.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MOSS_working_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 149-151 (MOSS_working_example.Rmd) 
Error: processing vignette 'MOSS_working_example.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MOSS_working_example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs     3.7Mb
    raster   2.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘motoRneuron.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: dygraphs
Quitting from lines 121-122 (motoRneuron.Rmd) 
Error: processing vignette 'motoRneuron.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘motoRneuron.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mountainplot_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 49-54 (mountainplot_examples.Rmd) 
Error: processing vignette 'mountainplot_examples.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mountainplot_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R   2.0Mb
Packages suggested but not available for checking:
  'CGHcall', 'aroma.affymetrix', 'aroma.cn', 'aroma.core',
  'aroma.light'
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Packages required but not available: 'TreeBUGS', 'runjags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Extracting simulation results from file:
/Volumes/Builds/packages/big-sur-arm64/results/4.1/mptools.Rcheck/mptools/example.mp
Extracting population metadata from file:
/Volumes/Builds/packages/big-sur-arm64/results/4.1/mptools.Rcheck/mptools/example.mp
Quitting from lines 136-140 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 93.4Mb
  sub-directories of 1Mb or more:
    libs  93.1Mb
Running examples in ‘mrbayes-Ex.R’ failed
The error most likely occurred in:

> ### Name: mr_egger_rjags
> ### Title: Bayesian implementation of the MR-Egger multivariate model with
> ###   choice of prior distributions fitted using JAGS.
> ### Aliases: mr_egger_rjags
> 
> ### ** Examples
> 
> fit <- mr_egger_rjags(bmi_insulin)
Error: Package "rjags" needed for this function to work. Please install it.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mrf2d-family.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘mrf2d-family.Rmd’

--- re-building ‘three-dimensions-on-mrf2d.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 69-70 (three-dimensions-on-mrf2d.Rmd) 
Error: processing vignette 'three-dimensions-on-mrf2d.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘three-dimensions-on-mrf2d.Rmd’

SUMMARY: processing the following file failed:
  ‘three-dimensions-on-mrf2d.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Packages required but not available: 'pcalg', 'WGCNA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   7.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsageOfMrSGUIDE.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 119-120 (UsageOfMrSGUIDE.Rmd) 
Error: processing vignette 'UsageOfMrSGUIDE.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘UsageOfMrSGUIDE.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sample-size-calcualtor-for-mrt.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 193-198 (sample-size-calcualtor-for-mrt.Rmd) 
Error: processing vignette 'sample-size-calcualtor-for-mrt.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sample-size-calcualtor-for-mrt.Rmd’

SUMMARY: processing the following file failed:
  ‘sample-size-calcualtor-for-mrt.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘msaR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 25-32 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘msaR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CheckingSynth.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘CheckingSynth.Rmd’

--- re-building ‘UsingTimeSeries.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘UsingTimeSeries.Rmd’

--- re-building ‘WorkingWithMSCMT.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 154-156 (WorkingWithMSCMT.Rmd) 
Error: processing vignette 'WorkingWithMSCMT.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘WorkingWithMSCMT.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   4.0Mb
    libs   4.4Mb
installed size is 57.4Mb
  sub-directories of 1Mb or more:
    libs  57.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mSHAP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘mSHAP.Rmd’

--- re-building ‘mshap_plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 65-69 (mshap_plots.Rmd) 
Error: processing vignette 'mshap_plots.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘mshap_plots.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
Error(s) in re-building vignettes:
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--- re-building ‘msmtools.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 324-325 (msmtools.Rmd) 
Error: processing vignette 'msmtools.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘msmtools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 23.1Mb
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    libs  22.0Mb
Error(s) in re-building vignettes:
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--- re-building ‘create_mtc_device.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building 'create_mtc_device.Rmd'

--- re-building ‘simulate_map_gcode.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 65-73 (simulate_map_gcode.Rmd) 
Error: processing vignette 'simulate_map_gcode.Rmd' failed with diagnostics:
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--- failed re-building 'simulate_map_gcode.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘workflow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 115-116 (workflow.Rmd) 
Error: processing vignette 'workflow.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘workflow.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘muHVT.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required namespace: deldir
Loading required namespace: Hmisc
Loading required namespace: splancs
Loading required namespace: conf.design
Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.
Quitting from lines 364-369 (muHVT.Rmd) 
Error: processing vignette 'muHVT.Rmd' failed with diagnostics:
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--- failed re-building ‘muHVT.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
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Packages suggested but not available for checking:
  'switchBox', 'BiocStyle', 'leukemiasEset'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 21-22 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘Tutorial.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
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--- re-building ‘lmer-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 172-184 (lmer-vignette.Rmd) 
Error: processing vignette 'lmer-vignette.Rmd' failed with diagnostics:
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--- failed re-building ‘lmer-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 133.0Mb
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    libs  132.7Mb
installed size is 152.2Mb
  sub-directories of 1Mb or more:
    doc     5.9Mb
    libs  145.1Mb
installed size is  7.2Mb
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    libs   5.8Mb
Package unavailable to check Rd xrefs: ‘ComplexHeatmap’
Error(s) in re-building vignettes:
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--- re-building ‘QuickStart.Rmd’ using knitr
Quitting from lines 96-97 (QuickStart.Rmd) 
Error: processing vignette 'QuickStart.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 44.8Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
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--- re-building ‘using_musica.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (using_musica.Rmd) 
Error: processing vignette 'using_musica.Rmd' failed with diagnostics:
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--- failed re-building ‘using_musica.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/mutossGUI.Rcheck/00install.out’ for details.
Running examples in ‘mutoss-Ex.R’ failed
The error most likely occurred in:

> ### Name: Qvalue
> ### Title: Storey's (2001) q-value Procedure...
> ### Aliases: Qvalue
> 
> ### ** Examples
> pval <- c(runif(50), runif(50, 0, 0.01))
> result <- Qvalue(pval)
Loading required package: qvalue
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘qvalue’
Package qvalue is required - should we install it?
Error in requireLibrary("qvalue") : 
  Required package qvalue should not be installed
Calls: Qvalue -> requireLibrary
Execution halted
installed size is  7.1Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘MVN.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 35-36 (MVN.Rmd) 
Error: processing vignette 'MVN.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘MVN.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Theory_and_Implementation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 101-133 (Theory_and_Implementation.Rmd) 
Error: processing vignette 'Theory_and_Implementation.Rmd' failed with diagnostics:
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--- failed re-building ‘Theory_and_Implementation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mvSLOUCH_Carnivorans.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
using cached file: ~/Library/Caches/R/rdryad/10_5061_dryad_77tm4.zip
date created (size, mb): 2021-05-03 14:05:14 (0.022)
Quitting from lines 1138-1143 (mvSLOUCH_Carnivorans.Rmd) 
Error: processing vignette 'mvSLOUCH_Carnivorans.Rmd' failed with diagnostics:
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--- failed re-building ‘mvSLOUCH_Carnivorans.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/mwa.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘mmod_tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.3     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   1.4.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
OpenMx may run faster if it is compiled to take advantage of multiple cores.
Quitting from lines 70-79 (mmod_tutorial.Rmd) 
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--- failed re-building ‘mmod_tutorial.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Myrrixjars.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Myrrix.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/N2R.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 31.8Mb
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    data     1.9Mb
    libs    28.6Mb
    models   1.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Error(s) in re-building vignettes:
--- re-building ‘batch-mode.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘batch-mode.Rmd’

--- re-building ‘brightness-timeseries.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘brightness-timeseries.Rmd’

--- re-building ‘single-images.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Quitting from lines 52-70 (single-images.Rmd) 
Error: processing vignette 'single-images.Rmd' failed with diagnostics:
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--- failed re-building ‘single-images.Rmd’

SUMMARY: processing the following file failed:
  ‘single-images.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘exploring-imputed-values.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 92-100 (exploring-imputed-values.Rmd) 
Error: processing vignette 'exploring-imputed-values.Rmd' failed with diagnostics:
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--- failed re-building ‘exploring-imputed-values.Rmd’

--- re-building ‘getting-started-w-naniar.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (getting-started-w-naniar.Rmd) 
Error: processing vignette 'getting-started-w-naniar.Rmd' failed with diagnostics:
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--- failed re-building ‘getting-started-w-naniar.Rmd’

--- re-building ‘naniar-visualisation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 29-32 (naniar-visualisation.Rmd) 
Error: processing vignette 'naniar-visualisation.Rmd' failed with diagnostics:
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--- failed re-building ‘naniar-visualisation.Rmd’

--- re-building ‘replace-with-na.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘replace-with-na.Rmd’

--- re-building ‘special-missing-values.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘special-missing-values.Rmd’

SUMMARY: processing the following files failed:
  ‘exploring-imputed-values.Rmd’ ‘getting-started-w-naniar.Rmd’
  ‘naniar-visualisation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
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    libs   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘natstrat.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 165-166 (natstrat.Rmd) 
Error: processing vignette 'natstrat.Rmd' failed with diagnostics:
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--- failed re-building ‘natstrat.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
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    data   4.6Mb
    doc    1.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘NBR-LM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 34-40 (NBR-LM.Rmd) 
Error: processing vignette 'NBR-LM.Rmd' failed with diagnostics:
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--- failed re-building ‘NBR-LM.Rmd’

--- re-building ‘NBR-LME.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 46-54 (NBR-LME.Rmd) 
Error: processing vignette 'NBR-LME.Rmd' failed with diagnostics:
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--- failed re-building ‘NBR-LME.Rmd’

SUMMARY: processing the following files failed:
  ‘NBR-LM.Rmd’ ‘NBR-LME.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘doRUnit.R’ [4s/5s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
  Number of errors: 0 
  Number of failures: 1 
  
   
  1 Test Suite : 
  nCal unit testing - 3 test functions, 0 errors, 1 failure
  FAILURE in test.bcrm: Error in checkEqualsNumeric(mean(fits$median.coef), 4.01789, tolerance = tolerance.jags) : 
    'is.NA' value mismatch: 0 in current 1 in target
  
  Error: 
  
  unit testing failed (#test failures: 1, #R errors: 0)
  
  In addition: There were 18 warnings (use warnings() to see them)
  Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] 329 - 233 ==   96.2
  [2] 197 - 293 ==  -96.2
  [3] 208 - 336 == -128.2
  [4] 318 - 190 ==  128.2
  ── Failure (test-file-functions.R:62:2): grid mappings are read and applied ────
  latlon.data$y not equal to lat.dat[indices].
  4/4 mismatches (average diff: 28)
  [1] 49.5 - 12.4 ==  37.1
  [2] 49.5 - 12.4 ==  37.1
  [3] 40.4 - 59.1 == -18.8
  [4] 40.4 - 59.1 == -18.8
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 45 ]
  Error: Test failures
  Execution halted
installed size is  8.8Mb
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    libs   8.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘v1-capture-first.Rmd’ using knitr
--- finished re-building ‘v1-capture-first.Rmd’

--- re-building ‘v2-capture-all.Rmd’ using knitr
--- finished re-building ‘v2-capture-all.Rmd’

--- re-building ‘v3-capture-melt.Rmd’ using knitr
Quitting from lines 102-115 (v3-capture-melt.Rmd) 
Error: processing vignette 'v3-capture-melt.Rmd' failed with diagnostics:
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--- failed re-building ‘v3-capture-melt.Rmd’

--- re-building ‘v4-comparisons.Rmd’ using knitr
Quitting from lines 103-116 (v4-comparisons.Rmd) 
Error: processing vignette 'v4-comparisons.Rmd' failed with diagnostics:
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--- failed re-building ‘v4-comparisons.Rmd’

SUMMARY: processing the following files failed:
  ‘v3-capture-melt.Rmd’ ‘v4-comparisons.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.2Mb
Packages required but not available:
  'genefilter', 'graphite', 'ndexr', 'org.Hs.eg.db', 'RCy3'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘developingNetjack.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘developingNetjack.Rmd’

--- re-building ‘netjackIntro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 147-156 (netjackIntro.Rmd) 
Error: processing vignette 'netjackIntro.Rmd' failed with diagnostics:
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--- failed re-building ‘netjackIntro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
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    doc    1.0Mb
    libs   4.8Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   7.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 72-73 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘quickstart_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
NetworkInference: Inferring latent diffusion networks.
Version 1.2.4
copyright (c) 2016, Fridolin Linder, Pennsylvania State University
                    Bruce Desmarais, Pennsylvania State University
For citation information, type citation("NetworkInference").
Type help("NetworkInference") to get started.

--- finished re-building ‘quickstart_vignette.Rmd’

--- re-building ‘tutorial_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
NetworkInference: Inferring latent diffusion networks.
Version 1.2.4
copyright (c) 2016, Fridolin Linder, Pennsylvania State University
                    Bruce Desmarais, Pennsylvania State University
For citation information, type citation("NetworkInference").
Type help("NetworkInference") to get started.


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 188-190 (tutorial_vignette.Rmd) 
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SUMMARY: processing the following file failed:
  ‘tutorial_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘network_scaleup.Rmd’ using docco_linear
Loading required package: plyr
Loading required package: dplyr

Attaching package: 'dplyr'

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

    arrange, count, desc, failwith, id, mutate, rename, summarise,
    summarize

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: functional
Loading required package: stringr
Quitting from lines 221-222 (network_scaleup.Rmd) 
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--- failed re-building ‘network_scaleup.Rmd’

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

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

Packages suggested but not available for checking: 'graphite', 'NFPdata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘nhstplot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 44-45 (nhstplot.Rmd) 
Error: processing vignette 'nhstplot.Rmd' failed with diagnostics:
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--- failed re-building ‘nhstplot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              6.1Mb
    classic-bugs   1.5Mb
    include        5.7Mb
    libs          18.4Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  PC 5 starting column: 2..
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-uscrime.R:68:3): SVD, NIPALS and EMPCA results match for complete uscrime data ──
  `avg_angle` is not strictly less than `tol`. Difference: NaN
  Backtrace:
      █
   1. └─nipals:::expect_aligned(m1s$u, m1e$scores) test-uscrime.R:68:2
   2.   └─testthat::expect_lt(avg_angle, tol) setup-expectations.R:22:2
  
  [ FAIL 1 | WARN 1 | SKIP 2 | PASS 27 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘DataInBrief.Rmd’ using knitr
Quitting from lines 938-948 (DataInBrief.Rmd) 
Error: processing vignette 'DataInBrief.Rmd' failed with diagnostics:
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--- failed re-building ‘DataInBrief.Rmd’

--- re-building ‘JEMBE.Rmd’ using knitr
Quitting from lines 468-479 (JEMBE.Rmd) 
Error: processing vignette 'JEMBE.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘JEMBE.Rmd’

SUMMARY: processing the following files failed:
  ‘DataInBrief.Rmd’ ‘JEMBE.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'a4Core', 'MLInterfaces'

Package suggested but not available for checking: ‘ALL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘geocode.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Package required but not available: ‘symengine’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
  DIRsubrout.c:505:10: warning: explicitly assigning value of variable of type 'integer' (aka 'int') to itself [-Wself-assign]
  hybrid.c:91:12: warning: 'nlopt_minimize' is deprecated [-Wdeprecated-declarations]
  newuoa.c:184:9: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
  newuoa.c:1241:10: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
  general.c:134:38: warning: 'syscall' is deprecated: first deprecated in macOS 10.12 - syscall(2) is unsupported; please switch to a supported interface. For SYS_kdebug_trace use kdebug_signpost(). [-Wdeprecated-declarations]
  ./f77funcs.h:57:14: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
  ./f77funcs.h:96:6: warning: 'nlopt_get_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
  ./f77funcs.h:104:6: warning: 'nlopt_set_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
  ./f77funcs.h:109:13: warning: 'nlopt_get_stochastic_population' is deprecated [-Wdeprecated-declarations]
  ./f77funcs.h:113:6: warning: 'nlopt_set_stochastic_population' is deprecated [-Wdeprecated-declarations]
  testopt.cpp:218:11: warning: 'nlopt_minimize' is deprecated [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/nloptr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/NLPutils.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘nlstimedist.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 150-151 (nlstimedist.Rmd) 
Error: processing vignette 'nlstimedist.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘nlstimedist.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 123-150 (Examples.Rmd) 
Error: processing vignette 'Examples.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘DataCreate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 404-416 (DataCreate.Rmd) 
Error: processing vignette 'DataCreate.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘DataCreate.Rmd’

--- re-building ‘NMdata-FAQ.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘NMdata-FAQ.Rmd’

--- re-building ‘NMscanData.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 330-338 (NMscanData.Rmd) 
Error: processing vignette 'NMscanData.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘NMscanData.Rmd’

SUMMARY: processing the following files failed:
  ‘DataCreate.Rmd’ ‘NMscanData.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Error(s) in re-building vignettes:
--- re-building ‘getting_started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: testthat

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 81-95 (getting_started.Rmd) 
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘getting_started.Rmd’

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

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

> ### Name: EF
> ### Title: Ensemble Filter
> ### Aliases: EF EF.default EF.formula
> 
> ### ** Examples
> 
> data(iris)
> # We fix a seed since there exists a random partition for the ensemble
> set.seed(1)
> out <- EF(Species~., data = iris, consensus = FALSE)
Error(s) in re-building vignettes:
  ...
--- re-building ‘NoiseFiltersR.Rnw’ using knitr
Packages required but not available: 'GenomicRanges', 'Rsamtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-work-and-health-nomis-indicators.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 194-365 (Introduction-to-work-and-health-nomis-indicators.Rmd) 
Error: processing vignette 'Introduction-to-work-and-health-nomis-indicators.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction-to-work-and-health-nomis-indicators.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 182-207 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘Introduction-to-work-and-health-nomis-indicators.Rmd’
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Error(s) in re-building vignettes:
--- re-building ‘GOFvignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: gridExtra
Quitting from lines 28-30 (GOFvignette.Rmd) 
Error: processing vignette 'GOFvignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘GOFvignette.Rmd’

--- re-building ‘VPCvignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: gridExtra
Quitting from lines 42-47 (VPCvignette.Rmd) 
Error: processing vignette 'VPCvignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘VPCvignette.Rmd’

SUMMARY: processing the following files failed:
  ‘GOFvignette.Rmd’ ‘VPCvignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Packages suggested but not available for checking: 'treeio', 'ggtree'
Package unavailable to check Rd xrefs: ‘treeio’
Packages required but not available: 'EBImage', 'bioimagetools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs  19.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘NutrienTrackeR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 146-147 (NutrienTrackeR.Rmd) 
Error: processing vignette 'NutrienTrackeR.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘NutrienTrackeR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘README.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 64-82 (README.Rmd) 
Error: processing vignette 'README.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘README.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Errors in running code in vignettes:
when running code in ‘oaih.Rnw’
  ...

> baseurl <- "http://epub.wu.ac.at/cgi/oai2"

> if (inherits(tryCatch(oaih_identify(baseurl), error = identity), 
+     "error")) q()
> proc.time()
   user  system elapsed 
  0.161   0.031   0.484 

... incomplete output.  Crash?

  ‘oaih.Rnw’ using ‘UTF-8’... failed to complete the test
Error(s) in re-building vignettes:
  ...
--- re-building ‘guide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 375-382 (guide.Rmd) 
Error: processing vignette 'guide.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘guide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    extdata   1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘integration_shiny.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘integration_shiny.Rmd’

--- re-building ‘oceanis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 73-82 (oceanis.Rmd) 
Error: processing vignette 'oceanis.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘oceanis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.6Mb
    test_files   4.2Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.8Mb
    libs   4.0Mb
Running examples in ‘ODB-Ex.R’ failed
The error most likely occurred in:

> ### Name: ODB-package
> ### Title: Open Document Databases (.odb) Management
> ### Aliases: ODB-package ODB
> ### Keywords: package
> 
> ### ** Examples
> 
> 
>   ## CONNECTION ##
>   
>   # Creation of a new .odb database
>   odbFile <- tempfile(fileext=".odb")
>   odb.create(odbFile, overwrite="do")
> 
>   # Connection to the file
>   odb <- odb.open(odbFile)
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 98-104 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘oddsratio.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 95-98 (oddsratio.Rmd) 
Error: processing vignette 'oddsratio.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘oddsratio.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 103.3Mb
  sub-directories of 1Mb or more:
    libs  102.8Mb
Running ‘testthat.R’ [5s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   24. │     └─grid::pushViewport(vp, recording = FALSE)
   25. │       └─base::lapply(vps, push.vp, recording)
   26. │         ├─grid:::FUN(X[[i]], ...)
   27. │         └─grid:::push.vp.vpTree(X[[i]], ...)
   28. │           ├─grid:::push.vp(vp$parent, recording)
   29. │           └─grid:::push.vp.viewport(vp$parent, recording)
   30. │             └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   31. └─(function (x) ...
   32.   ├─grid::widthDetails(x)
   33.   └─grid:::widthDetails.text(x)
   34.     └─grid:::grid.Call(...)
  
  [ FAIL 1 | WARN 29 | SKIP 0 | PASS 451 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ojsr-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 115-130 (ojsr-vignette.Rmd) 
Error: processing vignette 'ojsr-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ojsr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘tinytest.R’ [23s/32s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  testValidate.R................   19 tests [0;32mOK[0m 
  testValidate.R................   19 tests [0;32mOK[0m 
  testValidate.R................   19 tests [0;32mOK[0m 
  testValidate.R................   20 tests [0;32mOK[0m 
  testValidate.R................   21 tests [0;32mOK[0m [0;34m0.2s[0m
  ----- FAILED[data]: testApp.R<434--437>
   call| expect_identical_xl(getFavicons("https://reactome.org/content/detail/"), 
   call| -->    "https://reactome.org//templates/favourite/favicon.ico")
   diff| [33m<[39m [33mtarget[39m                                                     
   diff| [34m>[39m [34mcurrent[39m                                                    
   diff| [36m@@ 1 / 1 @@                                                  [39m
   diff| [33m<[39m [90m[1] [39m[33m"https://reactome.org//templates/favourite/favicon.ico"[39m[90m[39m
   diff| [34m>[39m [90m[1] [39m[34m"https://icons.duckduckgo.com/ip3/reactome.org.ico"[39m[90m[39m    
  Error: 1 out of 572 tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Omu_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning: `funs()` was deprecated in dplyr 0.8.0.
Please use a list of either functions or lambdas: 

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

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

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `group_by_()` was deprecated in dplyr 0.7.0.
Please use `group_by()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 266-269 (Omu_vignette.Rmd) 
Error: processing vignette 'Omu_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Omu_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Creating_Templated_Office_Workflows.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 138-151 (Creating_Templated_Office_Workflows.Rmd) 
Error: processing vignette 'Creating_Templated_Office_Workflows.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Creating_Templated_Office_Workflows.Rmd’

--- re-building ‘Custom_Office_Templates.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Custom_Office_Templates.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 48.2Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

No stratum defined - assigning all groups to single stratum "all"
Info: The group(s) IIT have undefined strata. Assigning first stratum all.
stratum_id not given, but only one stratum defined. Assigning first stratum.
Info: The group(s) IIT have undefined strata. Assigning first stratum all.
stratum_id not given, but only one stratum defined. Assigning first stratum.
Info: The group(s) IIT have undefined strata. Assigning first stratum all.
stratum_id not given, but only one stratum defined. Assigning first stratum.
stratum_id not given, but only one stratum defined. Assigning first stratum.
Info: The group(s) IIT have undefined strata. Assigning first stratum all.
stratum_id not given, but only one stratum defined. Assigning first stratum.
stratum_id not given, but only one stratum defined. Assigning first stratum.
Info: The group(s) IIT have undefined strata. Assigning first stratum all.
stratum_id not given, but only one stratum defined. Assigning first stratum.
stratum_id not given, but only one stratum defined. Assigning first stratum.
Quitting from lines 375-378 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
Undefined global functions or variables:
  optim par x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par")
  importFrom("stats", "optim")
to your NAMESPACE file.
Packages required but not available:
  'sva', 'GenomicFeatures', 'org.Hs.eg.db',
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'maftools', 'genefilter',
  'TCGAbiolinks', 'GenomicRanges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.6Mb
Error(s) in re-building vignettes:
--- re-building ‘Inbred_Based_Populations.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 350-352 (Inbred_Based_Populations.Rmd) 
Error: processing vignette 'Inbred_Based_Populations.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Inbred_Based_Populations.Rmd’

--- re-building ‘Introduction_R.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Introduction_R.Rmd’

--- re-building ‘Outcrossing_Populations.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 193-194 (Outcrossing_Populations.Rmd) 
Error: processing vignette 'Outcrossing_Populations.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Outcrossing_Populations.Rmd’

--- re-building ‘Overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Overview.Rmd’

SUMMARY: processing the following files failed:
  ‘Inbred_Based_Populations.Rmd’ ‘Outcrossing_Populations.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘btm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘btm.Rmd’

--- re-building ‘deploy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘deploy.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 481-482 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/OpenCL.Rcheck/00install.out’ for details.
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    libs   14.0Mb
    share  10.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘openland_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'https://zenodo.org/record/3685230/files/SaoLourencoBasin.rda?download=1'
Content type 'application/octet-stream' length 5309066 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

Quitting from lines 173-180 (openland_vignette.Rmd) 
Error: processing vignette 'openland_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘openland_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 220.8Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    libs    210.0Mb
    models    4.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/openNLPdata.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/openNLP.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘sop.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 304-316 (sop.Rmd) 
Error: processing vignette 'sop.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sop.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/OpenStreetMap.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/openVA.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      6.0Mb
Packages suggested but not available for checking:
  'gurobi', 'ggtree', 'Rsymphony', 'lpsymphony'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Package unavailable to check Rd xrefs: ‘ggtree’
Running ‘testthat.R’ [13s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   23. │     └─grid::pushViewport(vp, recording = FALSE)
   24. │       └─base::lapply(vps, push.vp, recording)
   25. │         ├─grid:::FUN(X[[i]], ...)
   26. │         └─grid:::push.vp.vpTree(X[[i]], ...)
   27. │           ├─grid:::push.vp(vp$parent, recording)
   28. │           └─grid:::push.vp.viewport(vp$parent, recording)
   29. │             └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   30. └─(function (x) ...
   31.   ├─grid::widthDetails(x)
   32.   └─grid:::widthDetails.text(x)
   33.     └─grid:::grid.Call(...)
  
  [ FAIL 4 | WARN 37 | SKIP 40 | PASS 1457 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'GO.db', 'org.At.tair.db'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/OptimalRerandExpDesigns.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘index.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘index.Rmd’

--- re-building ‘presentation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 39-49 (presentation.Rmd) 
Error: processing vignette 'presentation.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘presentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘optparse.Rrst’ using knitr
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
--- failed re-building ‘optparse.Rrst’

SUMMARY: processing the following file failed:
  ‘optparse.Rrst’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [140s/170s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  • Reference data 0.5.17 not available (1)
  • Reference data 0.5.18 not available (1)
  • Reference data 0.5.4 not available (2)
  • Reference data 0.6.0 not available (9)
  • vault is not enabled (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-testing.R:8:3): orderly_example can be quiet ──────────────────
  `orderly_example("minimal", run_demo = TRUE, quiet = TRUE)` produced warnings.
  
  [ FAIL 1 | WARN 11326 | SKIP 85 | PASS 1506 ]
  Error: Test failures
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Package suggested but not available for checking: ‘IsoGene’
Error(s) in re-building vignettes:
  ...
--- re-building ‘orf_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 209-211 (orf_vignette.Rmd) 
Error: processing vignette 'orf_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘orf_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘OrgMassSpecR-examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-68 (OrgMassSpecR-examples.Rmd) 
Error: processing vignette 'OrgMassSpecR-examples.Rmd' failed with diagnostics:
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--- failed re-building ‘OrgMassSpecR-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘OrgMassSpecR-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ormPlot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 84-85 (ormPlot.Rmd) 
Error: processing vignette 'ormPlot.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ormPlot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/oRus.Rcheck/00install.out’ for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   7.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/OSMscale.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘OTclust.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 87-91 (OTclust.Rmd) 
Error: processing vignette 'OTclust.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘OTclust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-outcomerate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 162-176 (intro-to-outcomerate.Rmd) 
Error: processing vignette 'intro-to-outcomerate.Rmd' failed with diagnostics:
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--- failed re-building ‘intro-to-outcomerate.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘outlierensembles.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-46 (outlierensembles.Rmd) 
Error: processing vignette 'outlierensembles.Rmd' failed with diagnostics:
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--- failed re-building ‘outlierensembles.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘DrawingO3plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-32 (DrawingO3plots.Rmd) 
Error: processing vignette 'DrawingO3plots.Rmd' failed with diagnostics:
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--- failed re-building ‘DrawingO3plots.Rmd’

--- re-building ‘MultTolLevels.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-35 (MultTolLevels.Rmd) 
Error: processing vignette 'MultTolLevels.Rmd' failed with diagnostics:
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--- failed re-building ‘MultTolLevels.Rmd’

--- re-building ‘PCPsO3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 30-53 (PCPsO3.Rmd) 
Error: processing vignette 'PCPsO3.Rmd' failed with diagnostics:
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--- failed re-building ‘PCPsO3.Rmd’

--- re-building ‘xtraO3methods.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘xtraO3methods.Rmd’

SUMMARY: processing the following files failed:
  ‘DrawingO3plots.Rmd’ ‘MultTolLevels.Rmd’ ‘PCPsO3.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error(s) in re-building vignettes:
--- re-building ‘overviewR_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: knitr
Loading required package: devtools
Loading required package: usethis
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 268-270 (overviewR_vignette.Rmd) 
Error: processing vignette 'overviewR_vignette.Rmd' failed with diagnostics:
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--- failed re-building ‘overviewR_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘OVtool.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: twang
To reproduce results from prior versions of the twang package, please see the version="legacy" option described in the documentation.
Quitting from lines 245-246 (OVtool.Rmd) 
Error: processing vignette 'OVtool.Rmd' failed with diagnostics:
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--- failed re-building ‘OVtool.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  OwenQ:::RcppOwenCDF4(1, 3, t2, 1000, delta2, algo) not equal to ptOwen(t2, 1, delta2).
  1/1 mismatches
  [1] 0.151 - 0.151 == -2.78e-17
  ── Failure (test-pOwen_algo2.R:100:3): powen4 - delta1=Inf ─────────────────────
  OwenQ:::RcppOwenCDF4(1, 3, t2, 1000, delta2, algo) not equal to ptOwen(t2, 1, delta2).
  1/1 mismatches
  [1] 0.151 - 0.151 == -2.78e-17
  ── Failure (test-ptOwen.R:24:3): ptOwen = Q2 for R=0 ───────────────────────────
  ptOwen(2, 1, 3) not equal to OwenQ2(1, 2, 3, 0).
  1/1 mismatches
  [1] 0.18 - NaN == NaN
  
  [ FAIL 10 | WARN 0 | SKIP 0 | PASS 285 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'https://c14.arch.ox.ac.uk/OxCalDistribution.zip'
Content type 'application/zip' length 4135026 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

OxCal v4.4.4 (c) Bronk Ramsey (2021)
Quitting from lines 24-31 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
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--- failed re-building ‘basic-usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Packages required but not available:
  'genbankr', 'GenomicAlignments', 'GenomicRanges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("padr")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_span.R:96:3): assure_greater_than_max_x works properly ────────
  assure_greater_than_max_x(max_x_date, end_val_posix, "day") not equal to as.POSIXct("2016-10-21 14:39:04").
  1/1 mismatches
  [1] 2016-10-21 15:39:04 - 2016-10-21 14:39:04 == 1 hours
  ── Failure (test_span.R:98:3): assure_greater_than_max_x works properly ────────
  assure_greater_than_max_x(max_x_posix, end_val_posix, "day") not equal to as.POSIXct("2016-10-21 14:39:04").
  1/1 mismatches
  [1] 2016-10-21 15:39:04 - 2016-10-21 14:39:04 == 1 hours
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 604 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_pafr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 83-91 (Introduction_to_pafr.Rmd) 
Error: processing vignette 'Introduction_to_pafr.Rmd' failed with diagnostics:
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--- failed re-building ‘Introduction_to_pafr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘N2R’

Packages suggested but not available for checking:
  'BiocParallel', 'GO.db', 'org.Dr.eg.db', 'org.Hs.eg.db',
  'org.Mm.eg.db', 'p2data', 'pcaMethods', 'scde'

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

Package suggested but not available for checking: ‘DECIPHER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘h-block-crossvalidation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
This is rioja 0.9-26
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.3     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   2.0.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Warning in Merge(object$y, newdata, split = TRUE) :
  Some row names were changed to avoid duplicates.
# A tibble: 1 × 1
   RMSE
  <dbl>
1  1.15
Quitting from lines 103-115 (h-block-crossvalidation.Rmd) 
Error: processing vignette 'h-block-crossvalidation.Rmd' failed with diagnostics:
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--- failed re-building ‘h-block-crossvalidation.Rmd’

SUMMARY: processing the following file failed:
  ‘h-block-crossvalidation.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages which this enhances but not available for checking:
  'CorShrink', 'edgeR'
Package required but not available: ‘PAMmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    doc    9.3Mb
    libs  57.4Mb
Error(s) in re-building vignettes:
--- re-building ‘PandemicLP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'http://github.com/CovidLP/PandemicLP/raw/master/temp/PandemicLP.rda'
Content type 'application/octet-stream' length 5854806 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

Quitting from lines 55-57 (PandemicLP.Rmd) 
Error: processing vignette 'PandemicLP.Rmd' failed with diagnostics:
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--- failed re-building ‘PandemicLP.Rmd’

--- re-building ‘PandemicLP_SumRegions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'http://github.com/CovidLP/PandemicLP/raw/master/temp/PandemicLP_SumRegions.rda'
Content type 'application/octet-stream' length 13851069 bytes (13.2 MB)
==================================================
downloaded 13.2 MB

trying URL 'http://github.com/CovidLP/PandemicLP/raw/master/temp/PandemicLP_SumRegions.rda'
Content type 'application/octet-stream' length 13851069 bytes (13.2 MB)
==================================================
downloaded 13.2 MB

--- finished re-building ‘PandemicLP_SumRegions.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_panelmatch.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 31-36 (using_panelmatch.Rmd) 
Error: processing vignette 'using_panelmatch.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘using_panelmatch.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘panta-rhei.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-70 (panta-rhei.Rmd) 
Error: processing vignette 'panta-rhei.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘panta-rhei.Rmd’

SUMMARY: processing the following file failed:
  ‘panta-rhei.Rmd’

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

> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)
> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parallelplot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-26 (introduction-to-parallelplot.Rmd) 
Error: processing vignette 'introduction-to-parallelplot.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction-to-parallelplot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Simulating-Power.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
This is lavaan 0.6-9
lavaan is FREE software! Please report any bugs.

Attaching package: 'dplyr'

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

    collapse

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 116-126 (Simulating-Power.Rmd) 
Error: processing vignette 'Simulating-Power.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Simulating-Power.Rmd’

SUMMARY: processing the following file failed:
  ‘Simulating-Power.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘functionMaximization.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-33 (functionMaximization.Rmd) 
Error: processing vignette 'functionMaximization.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘functionMaximization.Rmd’

--- re-building ‘multiPointSampling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘multiPointSampling.Rmd’

--- re-building ‘tuningHyperparameters.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
  2.24 seconds

Starting Epoch 1 
  1) Fitting Gaussian Process...
  2) Running local optimum search...        3.925 seconds
  3) Running FUN 1 times in 1 thread(s)...  0.299 seconds

Starting Epoch 2 
  1) Fitting Gaussian Process...
  2) Running local optimum search...        1.338 seconds
  3) Running FUN 1 times in 1 thread(s)...  0.333 seconds

Starting Epoch 3 
  1) Fitting Gaussian Process...
  2) Running local optimum search...        7.347 seconds
  3) Running FUN 1 times in 1 thread(s)...  0.376 seconds



Warning in sink() : no sink to remove
--- finished re-building ‘tuningHyperparameters.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parcoords-.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction-to-parcoords-.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘parmsurvfit_vig.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 55-60 (parmsurvfit_vig.Rmd) 
Error: processing vignette 'parmsurvfit_vig.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘parmsurvfit_vig.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 20.3Mb
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    libs  19.9Mb
installed size is  7.0Mb
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    doc    1.2Mb
    libs   4.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_partR2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Matrix
Quitting from lines 131-137 (Using_partR2.Rmd) 
Error: processing vignette 'Using_partR2.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Using_partR2.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_partR2.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘bugfixes.R’ [2s/3s]
  Comparing ‘bugfixes.Rout’ to ‘bugfixes.Rout.save’ ... OK
  Running ‘constparty.R’ [2s/2s]
  Comparing ‘constparty.Rout’ to ‘constparty.Rout.save’ ... OK
  Running ‘regtest-MIA.R’ [1s/1s]
  Comparing ‘regtest-MIA.Rout’ to ‘regtest-MIA.Rout.save’ ... OK
  Running ‘regtest-cforest.R’ [4s/4s]
  Comparing ‘regtest-cforest.Rout’ to ‘regtest-cforest.Rout.save’ ... OK
  Running ‘regtest-ctree.R’ [1s/1s]
  Comparing ‘regtest-ctree.Rout’ to ‘regtest-ctree.Rout.save’ ... OK
  Running ‘regtest-glmtree.R’ [15s/18s]
  Comparing ‘regtest-glmtree.Rout’ to ‘regtest-glmtree.Rout.save’ ... OK
  Running ‘regtest-honesty.R’ [1s/1s]
  Running ‘regtest-lmtree.R’ [1s/2s]
  Running ‘regtest-nmax.R’ [1s/1s]
  Comparing ‘regtest-nmax.Rout’ to ‘regtest-nmax.Rout.save’ ... OK
  Running ‘regtest-node.R’ [1s/1s]
  Comparing ‘regtest-node.Rout’ to ‘regtest-node.Rout.save’ ... OK
  Running ‘regtest-party-random.R’ [1s/2s]
  Running ‘regtest-party.R’ [1s/1s]
Running the tests in ‘tests/regtest-party.R’ failed.
Last 13 lines of output:
  + 
  +     ## rpart/J48: GlaucomaM data
  +     data("GlaucomaM", package = "TH.data")
  +     w <- runif(nrow(GlaucomaM))
  +     fit <- rpart(Class ~ ., data = GlaucomaM, weights = w)
  +     pfit <- as.party(fit)
  +     print(all(predict(pfit, type = "node") == fit$where))
  +     tmp <- GlaucomaM[sample(1:nrow(GlaucomaM), 100),]
  +     print(all.equal(predict(fit, type = "prob", newdata = tmp), predict(pfit, type = "prob", newdata = tmp)))
  +     print(all.equal(predict(fit, type = "class", newdata = tmp), predict(pfit, newdata = tmp)))
  +     itree <- J48(Class ~ ., data = GlaucomaM)
  +     pitree <- as.party(itree)
  +     print(all.equal(predict(itree, newdata = tmp, type = "prob"), predict(pitree, newdata = tmp, type = "prob")))
  + }
  Loading required package: RWeka
Errors in running code in vignettes:
when running code in ‘constparty.Rnw’
  ...
       9 0.0729927 0.9270073

> if (require("RWeka")) {
+     j48 <- J48(Survived ~ ., data = ttnc)
+ } else {
+     j48 <- rpart(Survived ~ ., data = ttnc)
+ }
Loading required package: RWeka

... incomplete output.  Crash?

  ‘constparty.Rnw’... failed to complete the test
  ‘ctree.Rnw’ using ‘UTF-8’... [4s/4s] OK
  ‘mob.Rnw’... [4s/6s] OK
  ‘partykit.Rnw’... [1s/1s] OK
Error(s) in re-building vignettes:
sh: line 1: 53093 Trace/BPT trap: 5       '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpVkrj0h/filecf577c48252' 2>&1 < '/Volumes/Temp/tmp/RtmpVkrj0h/filecf577647d979'
--- re-building ‘constparty.Rnw’ using Sweave
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: RWeka
--- re-building ‘ctree.Rnw’ using Sweave
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: coin
Loading required package: survival
Loading required package: strucchange
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: Formula
Loading required package: modeltools
Loading required package: stats4

Attaching package: ‘party’

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

    cforest, ctree, ctree_control, edge_simple, mob,
    mob_control, node_barplot, node_bivplot, node_boxplot,
    node_inner, node_surv, node_terminal, varimp

--- finished re-building ‘ctree.Rnw’

--- re-building ‘mob.Rnw’ using Sweave
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required namespace: vcd
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: sandwich
--- finished re-building 'mob.Rnw'

--- re-building ‘partykit.Rnw’ using Sweave
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
--- finished re-building ‘partykit.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘passport.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 114-141 (passport.Rmd) 
Error: processing vignette 'passport.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘passport.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘patchwork.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 64-65 (patchwork.Rmd) 
Error: processing vignette 'patchwork.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘patchwork.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘pathfindR’
Packages required but not available: 'org.Hs.eg.db', 'KEGGgraph'

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

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

Package suggested but not available for checking: ‘biomaRt’

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

> ### Name: get_transition_info
> ### Title: Invoke the Transition Pairing Method
> ### Aliases: get_transition_info validate_transition_info_input
> ###   impute_trans recode_trans_names
> ### Keywords: internal
> 
> ### ** Examples
> 
> set.seed(100)
> predictions <- (sample(1:100)%%2)
> references  <- (sample(1:100)%%2)
> window_size <- 7
> get_transition_info(predictions, references, window_size)
Error(s) in re-building vignettes:
  ...
--- re-building ‘tpm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   3.6Mb
Packages required but not available: 'pbdMPI', 'pbdSLAP'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/pbdPROF.Rcheck/00install.out’ for details.
Running ‘address.R’ [0s/0s]
  Running ‘ports.R’ [0s/0s]
  Running ‘send_recv.R’ [0m/30m]
Running the tests in ‘tests/send_recv.R’ failed.
Last 13 lines of output:
  + {
  +   zmq.msg.send(indata, client_socket)
  +   c2s <- zmq.msg.recv(server_socket)
  +   stopifnot(all.equal(c2s, indata))
  + 
  +   zmq.send(server_socket, "ok")
  +   s2c <- zmq.recv(client_socket)
  +   stopifnot(all.equal(s2c$buf, "ok"))
  + }
  > 
  > tester("test")
  R_zmq_msg_recv errno: 4 strerror: Interrupted system call
  Error in unserialize(rmsg) : read error
  Calls: tester -> zmq.msg.recv -> unserialize
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pbo.Rmd’ using knitr
Quitting from lines 56-66 (pbo.Rmd) 
Error: processing vignette 'pbo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘pbo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      3.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/pcaL1.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 154.8Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
    libs  151.2Mb
Package required but not available: ‘safe’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 42.7Mb
  sub-directories of 1Mb or more:
    libs  41.5Mb
Error(s) in re-building vignettes:
--- re-building ‘PCMBase.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Failed with error:  'there is no package called 'ggtree''
Quitting from lines 37-53 (PCMBase.Rmd) 
Error: processing vignette 'PCMBase.Rmd' failed with diagnostics:
The ggtree installation did not succeed. The vignette cannot be built.
--- failed re-building ‘PCMBase.Rmd’

--- re-building ‘PCMCreateModel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Failed with error:  'there is no package called 'ggtree''
Quitting from lines 37-54 (PCMCreateModel.Rmd) 
Error: processing vignette 'PCMCreateModel.Rmd' failed with diagnostics:
The ggtree installation did not succeed. The vignette cannot be built.
--- failed re-building ‘PCMCreateModel.Rmd’

--- re-building ‘PCMParam.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘PCMParam.Rmd’

--- re-building ‘PCMTracePruning.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Failed with error:  'there is no package called 'ggtree''
Quitting from lines 37-59 (PCMTracePruning.Rmd) 
Error: processing vignette 'PCMTracePruning.Rmd' failed with diagnostics:
The ggtree installation did not succeed. The vignette cannot be built.
--- failed re-building ‘PCMTracePruning.Rmd’

SUMMARY: processing the following files failed:
  ‘PCMBase.Rmd’ ‘PCMCreateModel.Rmd’ ‘PCMTracePruning.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘qpcr_analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
`geom_smooth()` using formula 'y ~ x'
Quitting from lines 412-421 (qpcr_analysis.Rmd) 
Error: processing vignette 'qpcr_analysis.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘qpcr_analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs    7.8Mb
    share  12.8Mb
Error(s) in re-building vignettes:
--- re-building ‘pdi-example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'pdi'

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

    rf


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 114-117 (pdi-example.Rmd) 
Error: processing vignette 'pdi-example.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘pdi-example.Rmd’

SUMMARY: processing the following file failed:
  ‘pdi-example.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Examples.Rnw’ using knitr
--- finished re-building ‘Examples.Rnw’

--- re-building ‘Spatial_correlation.Rmd’ using knitr
Quitting from lines 105-123 (Spatial_correlation.Rmd) 
Error: processing vignette 'Spatial_correlation.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Spatial_correlation.Rmd’

--- re-building ‘Worst_case.Rmd’ using knitr
Quitting from lines 67-99 (Worst_case.Rmd) 
Error: processing vignette 'Worst_case.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Worst_case.Rmd’

SUMMARY: processing the following files failed:
  ‘Spatial_correlation.Rmd’ ‘Worst_case.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pedsuite.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 49-51 (pedsuite.Rmd) 
Error: processing vignette 'pedsuite.Rmd' failed with diagnostics:
Labels leave no room for the graph, reduce cex
--- failed re-building ‘pedsuite.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pedtools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 90-91 (pedtools.Rmd) 
Error: processing vignette 'pedtools.Rmd' failed with diagnostics:
Labels leave no room for the graph, reduce cex
--- failed re-building ‘pedtools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/pems.utils.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘globaltest’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Package required but not available: ‘survcomp’

Package suggested but not available for checking: ‘ptmixed’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 55.9Mb
  sub-directories of 1Mb or more:
    libs  54.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Perc.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 149-157 (Perc.Rmd) 
Error: processing vignette 'Perc.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Perc.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/permGPU.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘buildmer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-63 (buildmer.Rmd) 
Error: processing vignette 'buildmer.Rmd' failed with diagnostics:
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--- failed re-building ‘buildmer.Rmd’

--- re-building ‘permutes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 69-70 (permutes.Rmd) 
Error: processing vignette 'permutes.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘permutes.Rmd’

SUMMARY: processing the following files failed:
  ‘buildmer.Rmd’ ‘permutes.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    data   3.1Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/pguIMP.Rcheck/00install.out’ for details.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    help   1.2Mb
    libs   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ph2rand.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 573-576 (ph2rand.Rmd) 
Error: processing vignette 'ph2rand.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ph2rand.Rmd’

--- re-building ‘validation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘validation.Rmd’

SUMMARY: processing the following file failed:
  ‘ph2rand.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘seqLogo’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.5Mb
Package required but not available: ‘rjags’

Package suggested but not available for checking: ‘BiocParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.9Mb
Error(s) in re-building vignettes:
--- re-building ‘NER-MetaMAP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘NER-MetaMAP.Rmd’

--- re-building ‘NLP-NILE.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘NLP-NILE.Rmd’

--- re-building ‘example1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (example1.Rmd) 
Error: processing vignette 'example1.Rmd' failed with diagnostics:
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--- failed re-building ‘example1.Rmd’

--- re-building ‘example2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 63-64 (example2.Rmd) 
Error: processing vignette 'example2.Rmd' failed with diagnostics:
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--- failed re-building ‘example2.Rmd’

--- re-building ‘main.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘main.Rmd’

SUMMARY: processing the following files failed:
  ‘example1.Rmd’ ‘example2.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TutoPheVis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 150-158 (TutoPheVis.Rmd) 
Error: processing vignette 'TutoPheVis.Rmd' failed with diagnostics:
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--- failed re-building ‘TutoPheVis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 400-401 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
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--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘user-guide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
News at https://www.r4photobiology.info/

Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Loading required package: ggplot2
ggspectra: default axis labels updated
This is colorSpec.  Version: 1.2-1.  Author: Glenn Davis [aut, cre].  Built: R 4.1.0; ; 2021-07-24
 20:32:19 UTC; unix

Attaching package: 'colorSpec'

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

    normalize

Welcome to pavo 2! Take a look at the latest features (and update your bibliography) in our recent publication: Maia R., Gruson H., Endler J. A., White T. E. (2019) pavo 2: new tools for the spectral and spatial analysis of colour in R. Methods in Ecology and Evolution, 10, 1097-1107.
Loading required package: lattice
Loading required package: grid
Loading required package: xml2
Package hyperSpec, version 0.99-20201127

To get started, try
   vignette ("hyperspec")
   package?hyperSpec 
   vignette (package = "hyperSpec")

If you use this package please cite it appropriately.
   citation("hyperSpec")
will give you the correct reference.

The project homepage is http://hyperspec.r-forge.r-project.org



Attaching package: 'hyperSpec'

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

    bind

Read 3 items
Read 16 items
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
News at https://www.r4photobiology.info/
ggspectra: default axis labels updated
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
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--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: photobiology
News at https://www.r4photobiology.info/
Loading required package: ggplot2
ggspectra: default axis labels updated
Loading required package: photobiologyWavebands
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--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
News at https://www.r4photobiology.info/
ggspectra: default axis labels updated
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
News at https://www.r4photobiology.info/

Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

ggspectra: default axis labels updated
Quitting from lines 86-87 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
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--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
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    doc    3.4Mb
    help   1.1Mb
installed size is 45.5Mb
  sub-directories of 1Mb or more:
    libs  44.7Mb
Package required but not available: ‘LBE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   2.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  12.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘benchmarks.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘benchmarks.Rmd’

--- re-building ‘pglmm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘pglmm.Rmd’

--- re-building ‘plot-re.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 100-104 (plot-re.Rmd) 
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--- failed re-building ‘plot-re.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Error(s) in re-building vignettes:
--- re-building ‘debugme.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘debugme.Rmd’

--- re-building ‘digits.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘digits.Rmd’

--- re-building ‘extending.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘extending.Rmd’

--- re-building ‘numbers.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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--- re-building ‘printing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘printing.Rmd’

SUMMARY: processing the following file failed:
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Execution halted
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘pimeta.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
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SUMMARY: processing the following file failed:
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  ...
--- re-building ‘pinbasicVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
pin_ll(param = NULL, numbuys = NULL, numsells = NULL, factorization = "Lin_Ke")
initial_vals(numbuys = NULL, numsells = NULL, method = "HAC", length = 5,
    num_clust = 5, details = FALSE)
Quitting from lines 91-93 (./Examples/Examples.Rmd) 
Quitting from lines 70-71 (./Examples/Examples.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘pinochet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.2     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   1.4.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter()     masks stats::filter()
✖ dplyr::group_rows() masks kableExtra::group_rows()
✖ dplyr::lag()        masks stats::lag()
Linking to GEOS 3.9.1, GDAL 3.2.3, PROJ 7.2.1

Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'runjags', 'bayesmix', 'rjags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.0Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    "   <chr>                       <dbl>      <dbl> <chr>                 <dbl>"
    " 1 Toy Story                     100         95 A                        NA"
  ── Failure (test-data.R:77:3): Pixar academy head and tail ─────────────────────
  Results have changed from known value recorded in 'test-data_academy.txt'.
  
  old[1:4] vs new[1:4]
  - "# A tibble: 20 x 3"
  + "# A tibble: 20 × 3"
    "   film         award_type          status                  "
    "   <chr>        <chr>               <chr>                   "
    " 1 Toy Story    Animated Feature    Award not yet introduced"
  
  [ FAIL 8 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pixar_film_ratings.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 38-57 (pixar_film_ratings.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_pkggraph.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 34-58 (vignette_pkggraph.Rmd) 
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--- failed re-building ‘vignette_pkggraph.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  pki-x509.c:428:2: warning: 'CC_MD5' is deprecated: first deprecated in macOS 10.15 - This function is cryptographically broken and should not be used in security contexts. Clients should migrate to SHA256 (or stronger). [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/PKI.Rcheck/00install.out’ for details.
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Example_dataset_creation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Example_dataset_creation.Rmd’

--- re-building ‘Using_plantecowrap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 18-50 (Using_plantecowrap.Rmd) 
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--- failed re-building ‘Using_plantecowrap.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'GenomicRanges', 'VariantAnnotation', 'Rsamtools', 'rtracklayer',
  'SummarizedExperiment'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘testing-platowork.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

`summarise()` has grouped output by 'subject'. You can override using the `.groups` argument.
Quitting from lines 82-103 (testing-platowork.Rmd) 
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SUMMARY: processing the following file failed:
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Execution halted
Packages required but not available:
  'RGtk2', 'gWidgets2RGtk2', 'cairoDevice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'biomformat', 'phyloseq', 'Wrench'
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   9.9Mb
Packages unavailable to check Rd xrefs: ‘DESeq2’, ‘Wrench’
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_plotdap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘landmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘plotluck.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 36-39 (plotluck.Rmd) 
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--- failed re-building ‘plotluck.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  6.7Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 99-101 (examples.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plotrr-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 30-36 (plotrr-vignette.Rmd) 
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--- failed re-building ‘plotrr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘mixOmics’
Running examples in ‘PLSbiplot1-Ex.R’ failed
The error most likely occurred in:

> ### Name: Mag.Bmat.plot
> ### Title: Magnitude of the Partial Least Squares Regression (PLSR)
> ###   coefficients matrix
> ### Aliases: Mag.Bmat.plot
> 
> ### ** Examples
> 
> if(require(pls))
+ data(oliveoil, package="pls")
Loading required package: pls

Attaching package: ‘pls’

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

    loadings

> X = as.matrix(oliveoil$chemical, ncol=5)
> dimnames(X) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Acidity","Peroxide","K232","K270","DK")))
> Y = as.matrix(oliveoil$sensory, ncol=6)
> dimnames(Y) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Yellow","Green","Brown","Glossy","Transp","Syrup")))
> Mag.Bmat.plot(X, Y, algorithm=mod.SIMPLS, A=2)
> 
> #nutrimouse data
> if(require(mixOmics))
+ data(nutrimouse, package="mixOmics")
Loading required package: mixOmics
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mixOmics’
> X1 = as.matrix(nutrimouse$lipid, ncol=21)
Error in as.matrix(nutrimouse$lipid, ncol = 21) : 
  object 'nutrimouse' not found
Execution halted
Packages required but not available: 'mixOmics', 'survcomp'

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

Package suggested but not available for checking: ‘MSnbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘tinytest.R’ [1s/1s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  test_valuation.R..............   12 tests [0;32mOK[0m 
  test_valuation.R..............   13 tests [0;32mOK[0m [0;36m3ms[0m
  ----- FAILED[data]: test_position.R<49--49>
   call| expect_equal(as.numeric(res), 2:3)
   diff| Numeric: lengths (2, 3) differ
  ----- FAILED[data]: test_position.R<55--55>
   call| expect_equal(as.numeric(res), 0:1)
   diff| Numeric: lengths (2, 3) differ
  Error: 2 out of 679 tests failed
  In addition: Warning messages:
  1: In pReturns(x, t, period, complete.first, pad = pad) :
    max. timestamp (2015) does not match current year
  2: In pReturns(x, t, period, complete.first, pad = pad) :
    max. timestamp (2015) does not match current year
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pk-curves.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: MASS
Loading required package: stringr
Loading required package: magrittr
Loading required package: data.tree
Loading required package: DiagrammeR
Quitting from lines 63-102 (pk-curves.Rmd) 
Error: processing vignette 'pk-curves.Rmd' failed with diagnostics:
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--- failed re-building ‘pk-curves.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘pocketapi.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 181-193 (pocketapi.Rmd) 
Error: processing vignette 'pocketapi.Rmd' failed with diagnostics:
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--- failed re-building ‘pocketapi.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘GDP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-35 (GDP.Rmd) 
Error: processing vignette 'GDP.Rmd' failed with diagnostics:
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--- failed re-building ‘GDP.Rmd’

--- re-building ‘Precipitation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-38 (Precipitation.Rmd) 
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--- failed re-building ‘Precipitation.Rmd’

--- re-building ‘Tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 95-97 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
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--- failed re-building ‘Tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘GDP.Rmd’ ‘Precipitation.Rmd’ ‘Tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pointRes_functionality.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Quitting from lines 58-59 (pointRes_functionality.Rmd) 
Error: processing vignette 'pointRes_functionality.Rmd' failed with diagnostics:
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--- failed re-building ‘pointRes_functionality.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘hexSticker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘using_PolicyPortfolios.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Package 'PolicyPortfolios' version 0.2.2
Type 'citation("PolicyPortfolios")' for citing this R package
or its datasets in publications.
Quitting from lines 182-192 (using_PolicyPortfolios.Rmd) 
Error: processing vignette 'using_PolicyPortfolios.Rmd' failed with diagnostics:
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--- failed re-building ‘using_PolicyPortfolios.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gdd.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 44-48 (gdd.Rmd) 
Error: processing vignette 'gdd.Rmd' failed with diagnostics:
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--- failed re-building ‘gdd.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘crosstab3way.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 41-54 (crosstab3way.Rmd) 
Error: processing vignette 'crosstab3way.Rmd' failed with diagnostics:
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--- failed re-building ‘crosstab3way.Rmd’

--- re-building ‘crosstabs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 52-56 (crosstabs.Rmd) 
Error: processing vignette 'crosstabs.Rmd' failed with diagnostics:
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--- failed re-building ‘crosstabs.Rmd’

--- re-building ‘toplines.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 45-48 (toplines.Rmd) 
Error: processing vignette 'toplines.Rmd' failed with diagnostics:
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--- failed re-building ‘toplines.Rmd’

SUMMARY: processing the following files failed:
  ‘crosstab3way.Rmd’ ‘crosstabs.Rmd’ ‘toplines.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
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    R         2.1Mb
    extdata   1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘polyCub.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 103-104 (polyCub.Rmd) 
Error: processing vignette 'polyCub.Rmd' failed with diagnostics:
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--- failed re-building ‘polyCub.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘polyRAD’
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    R      7.1Mb
    data   4.7Mb
Package unavailable to check Rd xrefs: ‘polyRAD’
Packages required but not available:
  'pcaMethods', 'imputeLCMD', 'mixOmics', 'ropls'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 68-69 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   1.7Mb
Package required but not available: ‘pcaMethods’

Packages suggested but not available for checking:
  'Rsamtools', 'GenomicRanges', 'VariantAnnotation',
  'SummarizedExperiment', 'GenomicFeatures'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ucla-example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-64 (ucla-example.Rmd) 
Error: processing vignette 'ucla-example.Rmd' failed with diagnostics:
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--- failed re-building ‘ucla-example.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Three_node_exmaple.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: reshape2
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Quitting from lines 120-156 (Three_node_exmaple.Rmd) 
Error: processing vignette 'Three_node_exmaple.Rmd' failed with diagnostics:
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--- failed re-building ‘Three_node_exmaple.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 59.0Mb
  sub-directories of 1Mb or more:
    libs  58.7Mb
Package required but not available: ‘EmpiricalBrownsMethod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 179-184 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
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--- failed re-building ‘examples.Rmd’

--- re-building ‘intro-poped.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 158-159 (intro-poped.Rmd) 
Error: processing vignette 'intro-poped.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro-poped.Rmd’

SUMMARY: processing the following files failed:
  ‘examples.Rmd’ ‘intro-poped.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘lfa’
Packages unavailable to check Rd xrefs: ‘rags2ridges’, ‘ragt2ridges’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/PortfolioEffectEstim.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/PortfolioEffectHFT.Rcheck/00install.out’ for details.
Package required but not available: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PosteriorBootstrap.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 236-256 (PosteriorBootstrap.Rmd) 
Error: processing vignette 'PosteriorBootstrap.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘PosteriorBootstrap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/postGGIR.Rcheck/00install.out’ for details.
Packages unavailable to check Rd xrefs: ‘R2jags’, ‘rjags’, ‘jagsUI’
Package required but not available: ‘miscF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Package suggested but not available for checking: ‘PerfMeas’
Running examples in ‘prcbench-Ex.R’ failed
The error most likely occurred in:

> ### Name: ToolAUCCalculator
> ### Title: ToolAUCCalculator
> ### Aliases: ToolAUCCalculator
> 
> ### ** Examples
> 
> ## Initialization
> toolauccalc <- ToolAUCCalculator$new()
Running ‘testthat.R’ [15s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #' @importFrom prcbench
  > 
  > library(testthat)
  > 
  > test_check("prcbench")
  Loading required package: prcbench
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_prcr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 27-30 (introduction_to_prcr.Rmd) 
Error: processing vignette 'introduction_to_prcr.Rmd' failed with diagnostics:
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--- failed re-building ‘introduction_to_prcr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘PRDA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘PRDA.Rmd’

--- re-building ‘prospective.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘prospective.Rmd’

--- re-building ‘retrospective.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.2     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   1.4.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 162-170 (retrospective.Rmd) 
Error: processing vignette 'retrospective.Rmd' failed with diagnostics:
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--- failed re-building ‘retrospective.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘predict3d.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: predict3d
Loading required package: rgl
Quitting from lines 55-58 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
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--- failed re-building ‘predict3d.Rmd’

SUMMARY: processing the following file failed:
  ‘predict3d.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘prepplotOverview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 31-64 (prepplotOverview.Rmd) 
Error: processing vignette 'prepplotOverview.Rmd' failed with diagnostics:
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--- failed re-building ‘prepplotOverview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘interpolation-in-small-samples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-91 (interpolation-in-small-samples.Rmd) 
Error: processing vignette 'interpolation-in-small-samples.Rmd' failed with diagnostics:
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--- failed re-building ‘interpolation-in-small-samples.Rmd’

--- re-building ‘using-weighted-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘using-weighted-data.Rmd’

--- re-building ‘visualizing-psm-results.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 64-69 (visualizing-psm-results.Rmd) 
Error: processing vignette 'visualizing-psm-results.Rmd' failed with diagnostics:
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--- failed re-building ‘visualizing-psm-results.Rmd’

SUMMARY: processing the following files failed:
  ‘interpolation-in-small-samples.Rmd’ ‘visualizing-psm-results.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.9Mb
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    libs  10.4Mb
installed size is  7.5Mb
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    libs   7.3Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.9Mb
    libs  14.8Mb
Running examples in ‘PRISMA2020-Ex.R’ failed
The error most likely occurred in:

> ### Name: PRISMA_save
> ### Title: Save PRISMA2020 flow diagram
> ### Aliases: PRISMA_save
> 
> ### ** Examples
> 
> csvFile <- system.file("extdata", "PRISMA.csv", package = "PRISMA2020")
> data <- read.csv(csvFile);
> data <- PRISMA_data(data);
> plot <- PRISMA_flowdiagram(data,
+                 fontsize = 12,
+                 interactive = TRUE,
+                 previous = FALSE,
+                 other = TRUE);
> PRISMA_save(plot, filename = tempfile(), filetype="html");
Error in htmlwidgets::saveWidget(plotobj, file = tmp_html, title = tools::file_path_sans_ext(filename)) : 
  Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Calls: PRISMA_save -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘equivocal-zones.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'probably'

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

    as.factor, as.ordered


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building ‘equivocal-zones.Rmd’

--- re-building ‘where-to-use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'probably'

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

    as.factor, as.ordered


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 175-201 (where-to-use.Rmd) 
Error: processing vignette 'where-to-use.Rmd' failed with diagnostics:
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--- failed re-building ‘where-to-use.Rmd’

SUMMARY: processing the following file failed:
  ‘where-to-use.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Running ‘output.R’ [0s/0s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(procmaps)
  > 
  > test_check("procmaps")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-get.R:28:3): files exist ──────────────────────────────────────
  file.exists(paths) not equal to rep(TRUE, length(paths)).
  1484 element mismatches
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 10 ]
  Error: Test failures
  Execution halted
installed size is 12.2Mb
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    extdata   7.4Mb
    libs      3.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      3.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/proj4.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘quick_start.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Rcpp
Loading required package: rlang

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 51-52 (quick_start.Rmd) 
Error: processing vignette 'quick_start.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘quick_start.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘prevalence’
Packages suggested but not available for checking: 'ALDEx2', 'SDMTools'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.4Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
Packages suggested but not available for checking:
  'GOSemSim', 'org.Hs.eg.db'
Package suggested but not available for checking: ‘proDA’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.9Mb
Package required but not available: ‘aroma.light’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introdution_psda.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 98-100 (introdution_psda.Rmd) 
Error: processing vignette 'introdution_psda.Rmd' failed with diagnostics:
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--- failed re-building ‘introdution_psda.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/psData.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.4Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 58.5Mb
  sub-directories of 1Mb or more:
    libs  57.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 44-45 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ma_r.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 235-237 (ma_r.Rmd) 
Error: processing vignette 'ma_r.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ma_r.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 657-669 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following files failed:
  ‘ma_r.Rmd’ ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  34.9Mb
Package required but not available: ‘tweeDEseq’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.0Mb
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    doc        4.0Mb
    examples   2.6Mb
installed size is 57.1Mb
  sub-directories of 1Mb or more:
    libs  56.6Mb
installed size is 39.1Mb
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    libs  38.6Mb
Packages required but not available:
  'SummarizedExperiment', 'Rsamtools', 'GenomicFeatures',
  'GenomicAlignments'

Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘PupillometryR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 80-83 (PupillometryR.Rmd) 
Error: processing vignette 'PupillometryR.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dcmle', 'dclone'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
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--- re-building ‘pvaluefun.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 123-156 (pvaluefun.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
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--- re-building ‘pwr-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
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Error(s) in re-building vignettes:
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--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Quitting from lines 85-86 (Introduction.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  8.5Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/qCBA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/qdap.Rcheck/00install.out’ for details.
installed size is  5.3Mb
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    R   5.1Mb
installed size is 90.9Mb
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Error(s) in re-building vignettes:
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--- re-building ‘qgcomp-vignette.Rmd’ using knitr
Quitting from lines 234-242 (qgcomp-vignette.Rmd) 
Error: processing vignette 'qgcomp-vignette.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Running examples in ‘qgraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: centrality_auto
> ### Title: Automatic centrality statistics of graphs
> ### Aliases: centrality_auto
> ### Keywords: graphs centrality
> 
> ### ** Examples
> 
> set.seed(1)
> adj <- matrix(sample(0:1,10^2,TRUE,prob=c(0.8,0.2)),nrow=10,ncol=10)
> Q <- qgraph(adj)
> centrality_auto(Q)
Error(s) in re-building vignettes:
  ...
--- re-building ‘qicharts2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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    intersect, setdiff, setequal, union

Quitting from lines 34-40 (qicharts2.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 102.4Mb
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Error(s) in re-building vignettes:
--- re-building ‘Parameter_Guidelines.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Parameter_Guidelines.rmd’

--- re-building ‘User_Guide.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘User_Guide.rmd’

--- re-building ‘Example-full-nca-analysis.rmd’ using knitr
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--- failed re-building ‘Example-full-nca-analysis.rmd’

--- re-building ‘Example-stepwise-nca-analysis.rmd’ using knitr
Quitting from lines 121-135 (Example-stepwise-nca-analysis.rmd) 
Error: processing vignette 'Example-stepwise-nca-analysis.rmd' failed with diagnostics:
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SUMMARY: processing the following files failed:
  ‘Example-full-nca-analysis.rmd’ ‘Example-stepwise-nca-analysis.rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘qqboxplot-basic-usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

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Quitting from lines 39-50 (qqboxplot-basic-usage.Rmd) 
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--- re-building ‘qqboxplot-paper-replication.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

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Quitting from lines 39-78 (qqboxplot-paper-replication.Rmd) 
Error: processing vignette 'qqboxplot-paper-replication.Rmd' failed with diagnostics:
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--- failed re-building ‘qqboxplot-paper-replication.Rmd’

SUMMARY: processing the following files failed:
  ‘qqboxplot-basic-usage.Rmd’ ‘qqboxplot-paper-replication.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: qqplotr
Loading required package: ggplot2

Attaching package: 'qqplotr'

The following objects are masked from 'package:ggplot2':

    StatQqLine, stat_qq_line

Quitting from lines 101-107 (introduction.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘qrLMM’
installed size is 13.3Mb
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installed size is  5.1Mb
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installed size is 17.6Mb
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installed size is 11.5Mb
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Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(qualpalr)
  > 
  > test_check("qualpalr")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_plotting.R:13:3): plotting functions work as expected ─────────
  `dont_plot(f)` produced warnings.
  ── Failure (test_plotting.R:14:3): plotting functions work as expected ─────────
  `dont_plot(f, pairs)` produced warnings.
  ── Failure (test_plotting.R:15:3): plotting functions work as expected ─────────
  `dont_plot(f, pairs, colorspace = "DIN99d")` produced warnings.
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 46 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
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--- re-building ‘wilcox1973.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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Error(s) in re-building vignettes:
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--- re-building ‘quickstart.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Package version: 3.0.0
Unicode version: 13.0
ICU version: 67.1
Parallel computing: 8 of 8 threads used.
See https://quanteda.io for tutorials and examples.
Quitting from lines 153-164 (quickstart.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 12.1Mb
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    libs   7.9Mb
installed size is 10.5Mb
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Error(s) in re-building vignettes:
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--- re-building ‘quickReg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 131-162 (quickReg.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quint.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 107-109 (quint.Rmd) 
Error: processing vignette 'quint.Rmd' failed with diagnostics:
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--- failed re-building ‘quint.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘quokar.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


Attaching package: 'dplyr'

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

    combine

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 62-63 (quokar.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘qwraps2-data-sets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘qwraps2-data-sets.Rmd’

--- re-building ‘qwraps2-graphics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 38-67 (qwraps2-graphics.Rmd) 
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--- re-building ‘summary-statistics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘summary-statistics.Rmd’

SUMMARY: processing the following file failed:
  ‘qwraps2-graphics.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Package required but not available: ‘sysfonts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘BRugs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘r3dmol.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 34-66 (r3dmol.Rmd) 
Error: processing vignette 'r3dmol.Rmd' failed with diagnostics:
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--- failed re-building ‘r3dmol.Rmd’

--- re-building ‘style-functions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 43-49 (style-functions.Rmd) 
Error: processing vignette 'style-functions.Rmd' failed with diagnostics:
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--- failed re-building ‘style-functions.Rmd’

SUMMARY: processing the following files failed:
  ‘r3dmol.Rmd’ ‘style-functions.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'batchelor', 'DESeq2', 'SummarizedExperiment'
installed size is 10.1Mb
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    data   2.1Mb
    doc    5.8Mb
    libs   1.5Mb
installed size is  5.3Mb
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    data      2.2Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_radsafer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in dk_correct(half_life = 10, time_unit = "y", date1 = "2010-01-01") :
  Date mode only provides precision to the day. Use time_lapse mode if more precision is needed.
Warning in dk_correct(RN_select = "Sr-90", date1 = "2005-01-01", date2 = c("2009-01-01",  :
  Date mode only provides precision to the day. Use time_lapse mode if more precision is needed.
Warning in dk_correct(RN_select = "Cs-137", date1 = "2019-01-01", date2 = c("2009-01-01",  :
  Date mode only provides precision to the day. Use time_lapse mode if more precision is needed.
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
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Packages required but not available: 'gRbase', 'RBGL'

Package suggested but not available for checking: ‘KEGGgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rags2ridges', 'CGHbase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.9Mb
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    api           3.1Mb
    htmlwidgets   7.0Mb
Packages required but not available:
  'InterpretMSSpectrum', 'pcaMethods', 'MSnbase'

Package suggested but not available for checking: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Heatplus’
Package unavailable to check Rd xrefs: ‘Heatplus’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    help   1.2Mb
    libs   4.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Packages required but not available: 'RBGL', 'PerfMeas'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [14s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       █
    1. ├─testthat::expect_true(is.vector(getRapPackages())) test-miscellaneous-functions.R:4:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::is.vector(getRapPackages())
    5. └─rapbase::getRapPackages()
    6.   └─base::sapply(allPkg$Package, isPkgRapReg)
    7.     └─base::lapply(X = X, FUN = FUN, ...)
    8.       └─rapbase:::FUN(X[[i]], ...)
    9.         └─base::grepl(...)
   10.           └─base::is.factor(x)
  
  [ FAIL 1 | WARN 4 | SKIP 3 | PASS 85 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'GenomicRanges', 'coloc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rapidraker.Rcheck/00install.out’ for details.
Packages required but not available:
  'Rsamtools', 'GenomicRanges', 'GenomicAlignments'

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.9Mb
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    doc    1.4Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘Raquifer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 78-102 (Raquifer.Rmd) 
Error: processing vignette 'Raquifer.Rmd' failed with diagnostics:
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--- failed re-building ‘Raquifer.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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Error(s) in re-building vignettes:
  ...
--- re-building ‘RaSEn-demo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 96-98 (RaSEn-demo.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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    libs   8.3Mb
installed size is  7.4Mb
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installed size is 86.8Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘data-formats.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘data-formats.Rmd’

--- re-building ‘workflow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 63-64 (workflow.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'cairoDevice', 'rggobi', 'RGtk2', 'RODBC'
installed size is  8.8Mb
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    etc    1.9Mb
    po     1.2Mb
installed size is 14.6Mb
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    data   4.1Mb
    libs  10.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 22-26 (intro.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 20.1Mb
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    libs  19.5Mb
installed size is  7.6Mb
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installed size is 11.2Mb
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Error(s) in re-building vignettes:
--- re-building ‘Building_Benvos.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'rbenvo'

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

    filter

Quitting from lines 74-75 (Building_Benvos.Rmd) 
Error: processing vignette 'Building_Benvos.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Building_Benvos.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'rbenvo'

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

    filter

Quitting from lines 78-79 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘Building_Benvos.Rmd’ ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  42.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rbgs.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [77s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    6.     └─future.apply::future_Map(...)
    7.       └─future.apply::future_mapply(FUN = f, ..., SIMPLIFY = FALSE, future.label = future.label)
    8.         └─future.apply:::future_xapply(...)
    9.           ├─future::value(fs)
   10.           └─future:::value.list(fs)
   11.             ├─future::resolve(...)
   12.             └─future:::resolve.list(...)
   13.               ├─future::value(obj, stdout = FALSE, signal = FALSE)
   14.               └─future:::value.Future(obj, stdout = FALSE, signal = FALSE)
   15.                 ├─future::result(future)
   16.                 └─future:::result.MulticoreFuture(future)
  
  [ FAIL 1 | WARN 5 | SKIP 9 | PASS 46 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-61 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Errors in running code in vignettes:
when running code in ‘rbiouml.Rnw’
  ...

> x[, 5] <- x[, 3] + x[, 4]

> biouml.put("data/Collaboration/Demo/tmp/exp_data_1_sum", 
+     x)

  When sourcing ‘rbiouml.R’:
Error: Cannot create collection data/Collaboration/Demo/tmp/exp_data_1_sum
Reason: Connection to SQL server cannot be established. URL: jdbc:mysql://mysql-biouml:3306/research_Demo?allowLoadLocalInfile=true
Execution halted

  ‘rbiouml.Rnw’... failed
Error(s) in re-building vignettes:
  ...
--- re-building ‘rbiouml.Rnw’ using Sweave
Loading required package: RCurl
Loading required package: RJSONIO

Error: processing vignette 'rbiouml.Rnw' failed with diagnostics:
 chunk 5 
Error in queryJSON("/web/table/createTable", params = c(de = path, columns = toJSON(columns),  : 
  Cannot create collection data/Collaboration/Demo/tmp/exp_data_1_sum
Reason: Connection to SQL server cannot be established. URL: jdbc:mysql://mysql-biouml:3306/research_Demo?allowLoadLocalInfile=true

--- failed re-building ‘rbiouml.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rblpapi.Rcheck/00install.out’ for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rCBA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rcdklibs.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rcdk.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rChoiceDialogs.Rcheck/00install.out’ for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Running examples in ‘rCMA-Ex.R’ failed
The error most likely occurred in:

> ### Name: cmaCalcFitness
> ### Title: Calculate the fitness of a population.
> ### Aliases: cmaCalcFitness
> 
> ### ** Examples
> 
> cma <- cmaNew();
Packages required but not available:
  'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE'

Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘fuzzyrcmdrplugin.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 47-48 (fuzzyrcmdrplugin.Rmd) 
Error: processing vignette 'fuzzyrcmdrplugin.Rmd' failed with diagnostics:
Cluster setup failed. 1 worker of 1 failed to connect.
--- failed re-building ‘fuzzyrcmdrplugin.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘extrafont.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘extrafont.Rmd’

--- re-building ‘geom-stepribbon.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 38-84 (geom-stepribbon.Rmd) 
Error: processing vignette 'geom-stepribbon.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘geom-stepribbon.Rmd’

--- re-building ‘plot-km-requirement.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘plot-km-requirement.Rmd’

SUMMARY: processing the following file failed:
  ‘geom-stepribbon.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'ROpenOffice', 'RODBC'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.3Mb
    po    2.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rcplex.Rcheck/00install.out’ for details.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    include   6.2Mb
    libs      2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RcppClassic.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lib    3.3Mb
    libs   1.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      5.6Mb
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     25.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-RcppHungarian.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 109-110 (Introduction-to-RcppHungarian.Rmd) 
Error: processing vignette 'Introduction-to-RcppHungarian.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction-to-RcppHungarian.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-RcppHungarian.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RcppMeCab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RcppMLPACK.Rcheck/00install.out’ for details.
installed size is 44.2Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      29.1Mb
    libs     13.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      3.0Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      6.4Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    include        1.7Mb
    jsonexamples   3.8Mb
    libs          15.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rcrypt.Rcheck/00install.out’ for details.
Package required but not available: ‘SingleCellExperiment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: sf
Linking to GEOS 3.9.1, GDAL 3.2.3, PROJ 7.2.1

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 27-50 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rdca.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 141-171 (Rdca.Rmd) 
Error: processing vignette 'Rdca.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Rdca.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RDieHarder.Rcheck/00install.out’ for details.
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  20.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rdroolsjars.Rcheck/00install.out’ for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Error(s) in re-building vignettes:
--- re-building ‘readabs_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Environment variable 'R_READABS_PATH' is unset. Downloaded files will be saved in a temporary directory.
You can set 'R_READABS_PATH' at any time. To set it for the rest of this session, use
	Sys.setenv(R_READABS_PATH = <path>)

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 251-265 (readabs_vignette.Rmd) 
Error: processing vignette 'readabs_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘readabs_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘readrba.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Quitting from lines 93-97 (readrba.Rmd) 
Error: processing vignette 'readrba.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘readrba.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.5Mb
    doc    2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.1Mb
Error(s) in re-building vignettes:
--- re-building ‘recexcavAAR-vignette-1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-1.Rmd’

--- re-building ‘recexcavAAR-vignette-2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-2.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-2.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-2.Rmd’

--- re-building ‘recexcavAAR-vignette-3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-3.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-3.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-3.Rmd’

SUMMARY: processing the following files failed:
  ‘recexcavAAR-vignette-1.Rmd’ ‘recexcavAAR-vignette-2.Rmd’
  ‘recexcavAAR-vignette-3.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-jss2711.R:9:3): reproducibility check for recmapGA using a 4x4 checkerboard (Figure 7) ──
  Error: index error
  Backtrace:
      █
   1. └─base::lapply(...) test-jss2711.R:9:2
   2.   └─recmap:::FUN(X[[i]], ...)
   3.     └─recmap::recmapGA(Map = checkerboard(4), pmutation = 0.25, parallel = FALSE) test-jss2711.R:13:4
   4.       └─GA::ga(...)
   5.         └─GA:::crossover(object, parents)
   6.           └─GA:::gaperm_oxCrossover_Rcpp(object, parents)
  
  [ FAIL 1 | WARN 93 | SKIP 1 | PASS 23 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘recmap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: GA
Loading required package: foreach
Loading required package: iterators
Package 'GA' version 3.2.1
Type 'citation("GA")' for citing this R package in publications.

Attaching package: 'GA'

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

    de

Loading required package: Rcpp
Loading required package: sp
Quitting from lines 201-207 (recmap.Rmd) 
Error: processing vignette 'recmap.Rmd' failed with diagnostics:
index error
--- failed re-building ‘recmap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 128-139 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   3.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘reda-Recur.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘reda-Recur.Rmd’

--- re-building ‘reda-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 123-129 (reda-intro.Rmd) 
Error: processing vignette 'reda-intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘reda-intro.Rmd’

--- re-building ‘reda-simulate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘reda-simulate.Rmd’

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

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

Packages suggested but not available for checking:
  'BiocStyle', 'TCGAbiolinks', 'qvalue'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Running examples in ‘RefFreeEWAS-Ex.R’ failed
The error most likely occurred in:

> ### Name: RefFreeCellMixInitializeBySVD
> ### Title: Initialize Reference-Free Cell Mixture Projection by SVD
> ### Aliases: RefFreeCellMixInitializeBySVD
> 
> ### ** Examples
> 
> data(HNSCC)
> Y.shortTest <- Y.HNSCC.averageBetas[1:500,]
> mu.start.svd <- RefFreeCellMixInitializeBySVD(Y.shortTest)
> testArray2  <- RefFreeCellMixArrayWithCustomStart(Y.shortTest, mu.start=mu.start.svd,
+     Klist=1:3,iters=5)
Fitting K = 1 
Fitting K = 2 
Error in solve.QP(Dmat, t(Xmat[obs, ]) %*% Y[obs, i], Amat, b0vec) : 
  constraints are inconsistent, no solution!
Calls: RefFreeCellMixArrayWithCustomStart -> RefFreeCellMix -> projectMix -> solve.QP
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ref-icar-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.5-23, (SVN revision 1121)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.2.3, released 2021/04/27
Path to GDAL shared files: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/rgdal/gdal
GDAL binary built with GEOS: TRUE 
Loaded PROJ runtime: Rel. 7.2.1, January 1st, 2021, [PJ_VERSION: 721]
Path to PROJ shared files: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.4-5
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
Overwritten PROJ_LIB was /Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/rgdal/proj
Warning in OGRSpatialRef(dsn, layer, morphFromESRI = morphFromESRI, dumpSRS = dumpSRS,  :
  Discarded datum D_unknown in Proj4 definition: +proj=longlat +ellps=clrk66 +no_defs
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 124-131 (ref-icar-vignette.Rmd) 
Error: processing vignette 'ref-icar-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ref-icar-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   5.5Mb
Packages suggested but not available for checking: 'interval', 'Icens'
Package unavailable to check Rd xrefs: ‘interval’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Relectoral.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_remap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Linking to GEOS 3.9.1, GDAL 3.2.3, PROJ 7.2.1
Loading required package: nlme

Attaching package: 'nlme'

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

    collapse

This is mgcv 1.8-36. For overview type 'help("mgcv-package")'.
Quitting from lines 49-61 (Introduction_to_remap.Rmd) 
Error: processing vignette 'Introduction_to_remap.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction_to_remap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/REPPlab.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/REPPlabShiny.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘representr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: plyr
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 300-311 (representr.Rmd) 
Error: processing vignette 'representr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘representr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   8.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    libs      4.0Mb
    swagger   1.4Mb
Packages suggested but not available for checking:
  'gWidgets2RGtk2', 'cairoDevice', 'RGtk2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_To_retrodesign.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 91-92 (Intro_To_retrodesign.Rmd) 
Error: processing vignette 'Intro_To_retrodesign.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Intro_To_retrodesign.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [4s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      █
   1. ├─testthat::expect_error(runAllChunks("test-rmarkdown.Rmd"), NA) test-rmarkdown.R:14:4
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat:::.capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─retrosheet:::runAllChunks("test-rmarkdown.Rmd")
   7.   └─rmarkdown::render(rmd, output_file = tempR, quiet = TRUE) test-rmarkdown.R:10:8
   8.     └─rmarkdown::pandoc_available(required_pandoc, error = TRUE)
   9.       └─rmarkdown:::stop2(paste(msg, collapse = " "))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 59 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 97-103 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
installed size is 49.0Mb
  sub-directories of 1Mb or more:
    libs  47.7Mb
Error(s) in re-building vignettes:
--- re-building ‘rfm-customer-level-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    group_rows

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 116-117 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘rfm-customer-level-data.Rmd’

--- re-building ‘rfm-transaction-level-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    group_rows

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 113-114 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘rfm-transaction-level-data.Rmd’

SUMMARY: processing the following files failed:
  ‘rfm-customer-level-data.Rmd’ ‘rfm-transaction-level-data.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RFreak.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rfVarImpOOB-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 58-61 (rfVarImpOOB-vignette.Rmd) 
Error: processing vignette 'rfVarImpOOB-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘rfVarImpOOB-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 346.4Mb
  sub-directories of 1Mb or more:
    doc         3.4Mb
    libs      339.1Mb
    pictures    1.3Mb
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    libs  31.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      2.1Mb
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    libs  36.1Mb
Package unavailable to check Rd xrefs: ‘Rsymphony’
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    doc     1.7Mb
    fonts   1.5Mb
    libs    7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘WebGL.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- re-building ‘pkgdown.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘pkgdown.Rmd’

--- re-building ‘rgl.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- re-building ‘transparency.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘transparency.Rmd’

SUMMARY: processing the following files failed:
  ‘WebGL.Rmd’ ‘rgl.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'showtext', 'sysfonts'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rGroovy.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RGtk2.Rcheck/00install.out’ for details.
Running ‘RH2_basic_in_mem_tests.R’ [0s/0s]
Running the tests in ‘tests/RH2_basic_in_mem_tests.R’ failed.
Complete output:
  > library(RH2)
  Loading required package: chron
  Loading required package: RJDBC
  Loading required package: DBI
  Loading required package: rJava
  > 
  > con = dbConnect(H2(), "jdbc:h2:mem:")
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_rhandsontable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘intro_rhandsontable.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 40-46 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'ggtree'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("rhmmer")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-parse.R:11:3): read_tblout works ──────────────────────────────
  `read_tblout(tblout_file)` produced messages.
  ── Failure (test-parse.R:17:3): read_domtblout works ───────────────────────────
  `read_domtblout(domtblout_file)` produced messages.
  ── Failure (test-parse.R:27:3): files with no data do not fail ─────────────────
  `read_domtblout(empty_tblout_file)` produced messages.
  ── Failure (test-parse.R:28:3): files with no data do not fail ─────────────────
  `read_tblout(empty_domtblout_file)` produced messages.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quadratic_phase_coupling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 104-118 (quadratic_phase_coupling.Rmd) 
Error: processing vignette 'quadratic_phase_coupling.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘quadratic_phase_coupling.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rhpc.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ri2_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 42-57 (ri2_vignette.Rmd) 
Error: processing vignette 'ri2_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ri2_vignette.Rmd’

--- re-building ‘ri2_vs_ri.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘ri2_vs_ri.Rmd’

SUMMARY: processing the following file failed:
  ‘ri2_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘remotes’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RInside.Rcheck/00install.out’ for details.
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette_manuscript.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 148-149 (Vignette_manuscript.Rmd) 
Error: processing vignette 'Vignette_manuscript.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Vignette_manuscript.Rmd’

--- re-building ‘Vignette_newbieRusers.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 313-314 (Vignette_newbieRusers.Rmd) 
Error: processing vignette 'Vignette_newbieRusers.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Vignette_newbieRusers.Rmd’

SUMMARY: processing the following files failed:
  ‘Vignette_manuscript.Rmd’ ‘Vignette_newbieRusers.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  23.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rjags.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

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

> ### Name: Exceptions
> ### Title: Exception handling
> ### Aliases: Exceptions $.Throwable $<-.Throwable
> 
> ### ** Examples
> 
> ## Don't show: 
> .jinit()
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RJDemetra.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rjdmarkdown.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rjdqa.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package required but not available: ‘chopsticks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RJSDMX.Rcheck/00install.out’ for details.
Running examples in ‘rJython-Ex.R’ failed
The error most likely occurred in:

> ### Name: jython.assign
> ### Title: Assign and get variables in Python from R
> ### Aliases: jython.assign jython.get
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
> rJython <- rJython()
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rkafkajars.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rkafka.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RKEAjars.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RKEA.Rcheck/00install.out’ for details.
Running examples in ‘RKEEL-Ex.R’ failed
The error most likely occurred in:

> ### Name: C45_C
> ### Title: C45_C KEEL Classification Algorithm
> ### Aliases: C45_C R6_C45_C
> ### Keywords: classification
> 
> ### ** Examples
> 
> data_train <- RKEEL::loadKeelDataset("iris_train")
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/RKEELdata/datasets/> data_test <- RKEEL::loadKeelDataset("iris_test")
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/RKEELdata/datasets/> 
> #Create algorithm
> algorithm <- RKEEL::C45_C(data_train, data_test)
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
Packages suggested but not available for checking:
  'genefilter', 'golubEsets'
Error(s) in re-building vignettes:
  ...
--- re-building ‘a-quickstart-rkolada.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 114-128 (a-quickstart-rkolada.Rmd) 
Error: processing vignette 'a-quickstart-rkolada.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘a-quickstart-rkolada.Rmd’

--- re-building ‘introduction-to-rkolada.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 159-193 (introduction-to-rkolada.Rmd) 
Error: processing vignette 'introduction-to-rkolada.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction-to-rkolada.Rmd’

SUMMARY: processing the following files failed:
  ‘a-quickstart-rkolada.Rmd’ ‘introduction-to-rkolada.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rLFT_Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 56-66 (rLFT_Introduction.Rmd) 
Error: processing vignette 'rLFT_Introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘rLFT_Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 66.2Mb
  sub-directories of 1Mb or more:
    libs  65.5Mb
Package required but not available: ‘hdf5r’

Packages suggested but not available for checking:
  'GenomicRanges', 'org.Hs.eg.db', 'reactome.db', 'fgsea'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    rmd   8.2Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RMark.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rmcfs.Rcheck/00install.out’ for details.
installed size is 91.9Mb
  sub-directories of 1Mb or more:
    libs  91.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rmdpartials.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 16-22 (rmdpartials.Rmd) 
Error: processing vignette 'rmdpartials.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘rmdpartials.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RmecabKo.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   7.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs       1.4Mb
    minizinc   3.2Mb
Package required but not available: ‘ROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    libs  44.2Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RMOAjars.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RMOA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rmpi.Rcheck/00install.out’ for details.
installed size is 63.3Mb
  sub-directories of 1Mb or more:
    libs  62.8Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RNCBIEUtilsLibs.Rcheck/00install.out’ for details.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Package unavailable to check Rd xrefs: ‘pbdMPI’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 113.9Mb
  sub-directories of 1Mb or more:
    extdata    2.0Mb
    libs     111.8Mb
Packages required but not available: 'MassSpecWavelet', 'speaq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R  11.4Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Package required but not available: ‘gprege’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
Package required but not available: ‘beadarray’

Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    libs  31.2Mb
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    libs  36.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RODBC.Rcheck/00install.out’ for details.
Package required but not available: ‘RODBC’

Package suggested but not available for checking: ‘RODBC’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    extdata   2.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘romic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 111-118 (romic.Rmd) 
Error: processing vignette 'romic.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘romic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/ROracle.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   6.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rotations-intro.Rnw’ using knitr
Quitting from lines 324-336 (rotations-intro.Rnw) 
Error: processing vignette 'rotations-intro.Rnw' failed with diagnostics:
polygon edge not found
--- failed re-building ‘rotations-intro.Rnw’

SUMMARY: processing the following file failed:
  ‘rotations-intro.Rnw’

Error: Vignette re-building failed.
Execution halted
Running ‘tinytest.R’ [1s/1s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly = TRUE) ){
  +   home <- length(unclass(packageVersion("roundhouse"))[[1L]]) == 4
  +   tinytest::test_package("roundhouse", at_home = home)
  + }
  
  test_roundhouse.R.............    0 tests    
  test_roundhouse.R.............    1 tests [0;32mOK[0m Loading required namespace: magick
  Fontconfig error: Cannot load default config file
  Error in magick_image_annotate(image, text, gravity, location, degrees,  : 
    R: NonconformingDrawingPrimitiveDefinition `text' @ error/draw.c/RenderMVGContent/4405
  Calls: <Anonymous> ... eval -> kick -> <Anonymous> -> magick_image_annotate
  Execution halted
Package suggested but not available for checking: ‘rmarkdown’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   3.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rpanel.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rpcdsearch.Rcheck/00install.out’ for details.
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘NEWS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘NEWS.Rmd’

--- re-building ‘rpivotTableIntroduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘rpivotTableIntroduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   7.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rpoppler.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘introduction.Rmd’

--- re-building ‘visualization.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 29-33 (visualization.Rmd) 
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘visualization.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diagnostics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: survival
Quitting from lines 58-59 (diagnostics.Rmd) 
Error: processing vignette 'diagnostics.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘diagnostics.Rmd’

--- re-building ‘user_guide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: survival
Quitting from lines 44-52 (user_guide.Rmd) 
Error: processing vignette 'user_guide.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘user_guide.Rmd’

SUMMARY: processing the following files failed:
  ‘diagnostics.Rmd’ ‘user_guide.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  40.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rpsftm_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 141-143 (rpsftm_vignette.Rmd) 
Error: processing vignette 'rpsftm_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘rpsftm_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rpvt.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 115-172 (Rpvt.Rmd) 
Error: processing vignette 'Rpvt.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Rpvt.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘CoupledHarmonics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 40-42 (CoupledHarmonics.Rmd) 
Error: processing vignette 'CoupledHarmonics.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘CoupledHarmonics.Rmd’

--- re-building ‘CoupledHarmonics2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 40-42 (CoupledHarmonics2.Rmd) 
Error: processing vignette 'CoupledHarmonics2.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘CoupledHarmonics2.Rmd’

--- re-building ‘CoupledTwoLevelSystems.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘CoupledTwoLevelSystems.Rmd’

SUMMARY: processing the following files failed:
  ‘CoupledHarmonics.Rmd’ ‘CoupledHarmonics2.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 113.8Mb
  sub-directories of 1Mb or more:
    libs  113.3Mb
Running ‘RQuantlib.R’ [0s/0s]
Running the tests in ‘tests/RQuantlib.R’ failed.
Last 13 lines of output:
  +                             settleDate=as.Date('2002-2-15'),
  +                             dt=0.25,
  +                             interpWhat='discount', interpHow='loglinear')
  > discountCurve <- DiscountCurve(discountCurve.param, list(flat=0.05))
  > 
  > ZeroCouponBond(bond, discountCurve, dateparams)
  
   *** caught segfault ***
  address 0x0, cause 'invalid permissions'
  
  Traceback:
   1: ZeroBondWithRebuiltCurve(bond, c(discountCurve$table$date), discountCurve$table$zeroRates,     dateparams)
   2: ZeroCouponBond.default(bond, discountCurve, dateparams)
   3: ZeroCouponBond(bond, discountCurve, dateparams)
  An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rrdrand.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rrd.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rrr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (rrr.Rmd) 
Error: processing vignette 'rrr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘rrr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘RRRR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 106-107 (RRRR.Rmd) 
Error: processing vignette 'RRRR.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘RRRR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ragged.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 49-55 (ragged.Rmd) 
Error: processing vignette 'ragged.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ragged.Rmd’

--- re-building ‘rescaling_data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-56 (rescaling_data.Rmd) 
Error: processing vignette 'rescaling_data.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘rescaling_data.Rmd’

SUMMARY: processing the following files failed:
  ‘ragged.Rmd’ ‘rescaling_data.Rmd’

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

Package suggested but not available for checking: ‘biomaRt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Working_with_rsets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 131-134 (Working_with_rsets.Rmd) 
Error: processing vignette 'Working_with_rsets.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Working_with_rsets.Rmd’

--- re-building ‘rsample.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘rsample.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    dependencies  20.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RSCAT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RSclient.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 249-266 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Package suggested but not available for checking: ‘RSclient’
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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 31.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  29.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
installed size is 49.0Mb
  sub-directories of 1Mb or more:
    libs  48.4Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Package required but not available: ‘GMMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
installed size is 238.2Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    doc     4.5Mb
    libs  231.0Mb
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs  38.3Mb
Error(s) in re-building vignettes:
--- re-building ‘emaxmodel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Rcpp

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 52-53 (emaxmodel.Rmd) 
Error: processing vignette 'emaxmodel.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘emaxmodel.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 293.7Mb
  sub-directories of 1Mb or more:
    lib    30.0Mb
    libs  260.8Mb
installed size is 115.1Mb
  sub-directories of 1Mb or more:
    libs  113.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rsubgroup.Rcheck/00install.out’ for details.
installed size is 107.8Mb
  sub-directories of 1Mb or more:
    libs  107.4Mb
Running examples in ‘rsvg-Ex.R’ failed
The error most likely occurred in:

> ### Name: rsvg
> ### Title: Render SVG into Bitmap
> ### Aliases: rsvg rsvg_raw rsvg_webp rsvg_png rsvg_pdf rsvg_svg rsvg_ps
> 
> ### ** Examples
> 
> # create some svg
> options(example.ask=FALSE)
> tmp <- tempfile()
> svglite::svglite(tmp, width = 10, height = 7)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘systemfonts’
Calls: loadNamespace ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 33-35 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rsymphony.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R           2.1Mb
    bootstrap   1.6Mb
    data        2.2Mb
Error(s) in re-building vignettes:
--- re-building ‘reanalysis_rr98.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: rtdists
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: tidyr
Loading required package: purrr
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: binom
`summarise()` has grouped output by 'id', 'instruction'. You can override using the `.groups` argument.
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 29-52 (reanalysis_rr98.Rmd) 
Error: processing vignette 'reanalysis_rr98.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘reanalysis_rr98.Rmd’

SUMMARY: processing the following file failed:
  ‘reanalysis_rr98.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘tests.R’ [0s/0s]
Running the tests in ‘tests/tests.R’ failed.
Last 13 lines of output:
  > 
  > # Try trellis plots
  > 
  > # single page trellis objects
  > addPageBreak(rtf, width=11,height=8.5,omi=c(0.5,0.5,0.5,0.5))
  > 
  > p <- histogram( ~ height | voice.part, data = singer, xlab="Height")
  > addTrellisObject(rtf,trellis.object=p,width=10,height=7.5,res=png.res)
  Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  : 
    polygon edge not found
  Calls: addTrellisObject ... <Anonymous> -> widthDetails -> widthDetails.text -> grid.Call
  In addition: Warning message:
  In grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
    no font could be found for family "Arial"
  Execution halted
Errors in running code in vignettes:
when running code in ‘rtf.Rnw’
  ...
> print(p)

> addPlot(rtf, plot.fun = print, width = 5, height = 5, 
+     res = 300, p)
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"

  When sourcing ‘rtf.R’:
Error: polygon edge not found
Execution halted

  ‘rtf.Rnw’... failed
Error(s) in re-building vignettes:
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘overview.Rmd’

--- re-building ‘polar-gams.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 58-64 (polar-gams.Rmd) 
Error: processing vignette 'polar-gams.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘polar-gams.Rmd’

--- re-building ‘tongue-imaging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 86-87 (tongue-imaging.Rmd) 
Error: processing vignette 'tongue-imaging.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘tongue-imaging.Rmd’

--- re-building ‘transform-coord.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 55-60 (transform-coord.Rmd) 
Error: processing vignette 'transform-coord.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘transform-coord.Rmd’

SUMMARY: processing the following files failed:
  ‘polar-gams.Rmd’ ‘tongue-imaging.Rmd’ ‘transform-coord.Rmd’

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

Packages suggested but not available for checking: 'Gviz', 'rtracklayer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       3.3Mb
    projects   2.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  26.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RtutoR.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Error(s) in re-building vignettes:
--- re-building ‘rubias-fully-bayesian.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 93-111 (rubias-fully-bayesian.Rmd) 
Error: processing vignette 'rubias-fully-bayesian.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘rubias-fully-bayesian.Rmd’

--- re-building ‘rubias-overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 274-291 (rubias-overview.Rmd) 
Error: processing vignette 'rubias-overview.Rmd' failed with diagnostics:
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--- failed re-building ‘rubias-overview.Rmd’

--- re-building ‘rubias-underlying-data-structures.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘rubias-underlying-data-structures.Rmd’

SUMMARY: processing the following files failed:
  ‘rubias-fully-bayesian.Rmd’ ‘rubias-overview.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   3.1Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   8.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/runjags.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-runstats.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 177-193 (using-runstats.Rmd) 
Error: processing vignette 'using-runstats.Rmd' failed with diagnostics:
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--- failed re-building ‘using-runstats.Rmd’

SUMMARY: processing the following file failed:
  ‘using-runstats.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 49.4Mb
  sub-directories of 1Mb or more:
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Packages required but not available:
  'GSVAdata', 'clusterProfiler', 'edgeR', 'org.Hs.eg.db',
  'ComplexHeatmap', 'GSEABase', 'rWikiPathways'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 49.9Mb
  sub-directories of 1Mb or more:
    libs  49.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rviewgraph.Rcheck/00install.out’ for details.
installed size is 65.8Mb
  sub-directories of 1Mb or more:
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    libs     61.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RVowpalWabbit.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RWekajars.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RWeka.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RxnSim.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘symengine’
installed size is  7.7Mb
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installed size is 11.7Mb
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installed size is 11.7Mb
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installed size is 12.8Mb
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installed size is 13.7Mb
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installed size is 39.7Mb
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    include   2.4Mb
    libs     36.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sadists.Rnw’ using knitr
Loading required package: ggplot2
Loading required package: grid
Loading required package: polynom
`stat_bin()` using `bins = 30`. Pick better value with
`binwidth`.
large z may result in inaccurate quantiles
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 409-415 (sadists.Rnw) 
Error: processing vignette 'sadists.Rnw' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sadists.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘introduction.Rmd’

--- re-building ‘recreating_analyses.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 67-77 (recreating_analyses.Rmd) 
Error: processing vignette 'recreating_analyses.Rmd' failed with diagnostics:
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--- failed re-building ‘recreating_analyses.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 16.2Mb
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installed size is 19.8Mb
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installed size is 23.1Mb
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installed size is 48.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  44.7Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   4.4Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'org.Sc.sgd.db'
Error(s) in re-building vignettes:
--- re-building ‘custom-aggregation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘custom-aggregation.Rmd’

--- re-building ‘data-flags.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘data-flags.Rmd’

--- re-building ‘memory-and-parallelization.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘memory-and-parallelization.Rmd’

--- re-building ‘metadata-and-data-units.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘metadata-and-data-units.Rmd’

--- re-building ‘sapfluxnetr-quick-guide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 267-270 (sapfluxnetr-quick-guide.Rmd) 
Error: processing vignette 'sapfluxnetr-quick-guide.Rmd' failed with diagnostics:
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--- failed re-building ‘sapfluxnetr-quick-guide.Rmd’

--- re-building ‘sfn-data-classes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 202-210 (sfn-data-classes.Rmd) 
Error: processing vignette 'sfn-data-classes.Rmd' failed with diagnostics:
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--- failed re-building ‘sfn-data-classes.Rmd’

SUMMARY: processing the following files failed:
  ‘sapfluxnetr-quick-guide.Rmd’ ‘sfn-data-classes.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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installed size is  5.3Mb
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    doc    1.7Mb
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installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.6Mb
Error(s) in re-building vignettes:
--- re-building ‘Multipartite_EcologicalNetwork.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (Multipartite_EcologicalNetwork.Rmd) 
Error: processing vignette 'Multipartite_EcologicalNetwork.Rmd' failed with diagnostics:
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--- failed re-building ‘Multipartite_EcologicalNetwork.Rmd’

--- re-building ‘MultiplexNetwork_principle.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 143-162 (MultiplexNetwork_principle.Rmd) 
Error: processing vignette 'MultiplexNetwork_principle.Rmd' failed with diagnostics:
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--- failed re-building ‘MultiplexNetwork_principle.Rmd’

--- re-building ‘Multiplex_allianceNwar_case_study.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-53 (Multiplex_allianceNwar_case_study.Rmd) 
Error: processing vignette 'Multiplex_allianceNwar_case_study.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Multiplex_allianceNwar_case_study.Rmd’

--- re-building ‘SBM_fungus_tree_network.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 77-78 (SBM_fungus_tree_network.Rmd) 
Error: processing vignette 'SBM_fungus_tree_network.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘SBM_fungus_tree_network.Rmd’

SUMMARY: processing the following files failed:
  ‘Multipartite_EcologicalNetwork.Rmd’ ‘MultiplexNetwork_principle.Rmd’
  ‘Multiplex_allianceNwar_case_study.Rmd’ ‘SBM_fungus_tree_network.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Weibull-edges.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 124-127 (Weibull-edges.Rmd) 
Error: processing vignette 'Weibull-edges.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Weibull-edges.Rmd’

SUMMARY: processing the following file failed:
  ‘Weibull-edges.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sbo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 219-226 (sbo.Rmd) 
Error: processing vignette 'sbo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sbo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/SBRect.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MMR_Distribution.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 110-113 (MMR_Distribution.Rmd) 
Error: processing vignette 'MMR_Distribution.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MMR_Distribution.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/scagnostics.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘scatterpie.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Quitting from lines 52-54 (scatterpie.Rmd) 
Error: processing vignette 'scatterpie.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘scatterpie.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   3.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘scholar.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 70-76 (scholar.Rmd) 
Error: processing vignette 'scholar.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘scholar.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘theoffice.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 81-90 (theoffice.Rmd) 
Error: processing vignette 'theoffice.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘theoffice.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘scipub_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 201-204 (scipub_vignette.Rmd) 
Error: processing vignette 'scipub_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘scipub_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'GSVA', 'pcaMethods', 'ADAPTS'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘scoringutils.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-75 (scoringutils.Rmd) 
Error: processing vignette 'scoringutils.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘scoringutils.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ginhoux.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 61-62 (ginhoux.Rmd) 
Error: processing vignette 'ginhoux.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ginhoux.Rmd’

--- re-building ‘simulated-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-63 (simulated-data.Rmd) 
Error: processing vignette 'simulated-data.Rmd' failed with diagnostics:
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--- failed re-building ‘simulated-data.Rmd’

--- re-building ‘seurat.html.asis’ using asis
--- finished re-building ‘seurat.html.asis’

SUMMARY: processing the following files failed:
  ‘ginhoux.Rmd’ ‘simulated-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘demoscouter.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-51 (demoscouter.Rmd) 
Error: processing vignette 'demoscouter.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘demoscouter.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Details.Rmd’ using knitr
--- finished re-building ‘Details.Rmd’

--- re-building ‘Tutorial.Rmd’ using knitr
Loading required package: Rcpp
Loading required package: RcppProgress
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Quitting from lines 129-134 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
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--- failed re-building ‘Tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘oligoClasses’
Package required but not available: ‘RCy3’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   4.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SDEFSRpackage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 538-540 (SDEFSRpackage.Rmd) 
Error: processing vignette 'SDEFSRpackage.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘SDEFSRpackage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R   8.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘season-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 32-38 (season-vignette.Rmd) 
Error: processing vignette 'season-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘season-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  16.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘segclust.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 79-80 (segclust.Rmd) 
Error: processing vignette 'segclust.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘segclust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'flowMerge', 'flowClust'
Package required but not available: ‘cate’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   2.9Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs    19.5Mb
    models   1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SentimentAnalysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 67-91 (SentimentAnalysis.Rmd) 
Error: processing vignette 'SentimentAnalysis.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘SentimentAnalysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Packages required but not available: 'qvalue', 'widgetTools', 'R2jags'

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

Packages suggested but not available for checking:
  'SummarizedExperiment', 'DESeq2', 'airway', 'qvalue', 'edgeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  12.7Mb
Packages suggested but not available for checking:
  'GenomicAlignments', 'GenomicRanges', 'muscle', 'Rsamtools'
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   1.3Mb
Package required but not available: ‘copynumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
Packages suggested but not available for checking:
  'hdf5r', 'SummarizedExperiment', 'SingleCellExperiment', 'MAST',
  'DESeq2', 'GenomicRanges', 'rtracklayer', 'monocle'
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.7Mb
Package unavailable to check Rd xrefs: ‘Signac’
Running ‘testthat.R’ [19s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("Seurat")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (19)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_load_10X.R:34:1): (code run outside of `test_that()`) ───────────
  Error: Please install hdf5r to read HDF5 files
  Backtrace:
      █
   1. └─Seurat::Load10X_Spatial(data.dir = "../testdata/visium") test_load_10X.R:34:0
   2.   └─Seurat::Read10X_h5(...)
  
  [ FAIL 1 | WARN 9 | SKIP 19 | PASS 587 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sfcr_multis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 133-144 (sfcr_multis.Rmd) 
Error: processing vignette 'sfcr_multis.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sfcr_multis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘v1_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘v1_intro.Rmd’

--- re-building ‘v3_analyzing_landing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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

    filter

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

    layout

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 61-70 (v3_analyzing_landing.Rmd) 
Error: processing vignette 'v3_analyzing_landing.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘v3_analyzing_landing.Rmd’

SUMMARY: processing the following file failed:
  ‘v3_analyzing_landing.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 377.0Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    libs    370.2Mb
    sqlite    1.5Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sGMRFmix.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 37-41 (sGMRFmix.Rmd) 
Error: processing vignette 'sGMRFmix.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sGMRFmix.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.4Mb
Error(s) in re-building vignettes:
--- re-building ‘SGP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP.Rmd’

--- re-building ‘SGP_Data_Analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP_Data_Analysis.Rmd) 
Error: processing vignette 'SGP_Data_Analysis.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Analysis.Rmd’

--- re-building ‘SGP_Data_Preparation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP_Data_Preparation.Rmd) 
Error: processing vignette 'SGP_Data_Preparation.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Preparation.Rmd’

SUMMARY: processing the following files failed:
  ‘SGP.Rmd’ ‘SGP_Data_Analysis.Rmd’ ‘SGP_Data_Preparation.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘Dirichlet-elicitation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 69-72 (Dirichlet-elicitation.Rmd) 
Error: processing vignette 'Dirichlet-elicitation.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Dirichlet-elicitation.Rmd’

--- re-building ‘Multivariate-normal-copula.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-53 (Multivariate-normal-copula.Rmd) 
Error: processing vignette 'Multivariate-normal-copula.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Multivariate-normal-copula.Rmd’

--- re-building ‘SHELF-overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 70-71 (SHELF-overview.Rmd) 
Error: processing vignette 'SHELF-overview.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘SHELF-overview.Rmd’

SUMMARY: processing the following files failed:
  ‘Dirichlet-elicitation.Rmd’ ‘Multivariate-normal-copula.Rmd’
  ‘SHELF-overview.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    www   8.8Mb
Running ‘test-all.R’ [12s/20s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
   17. │ │ │   └─domain$wrapSync(expr)
   18. │ │ │     └─base::force(expr)
   19. │ │ └─withr::with_options(...)
   20. │ │   └─base::force(code)
   21. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
   22. ├─testthat::expect_equal(output$fixed$width, 300) test-test-server.R:427:4
   23. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   24. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   25. ├─output$fixed
   26. └─shiny:::`$.shinyoutput`(output, fixed)
   27.   └─.subset2(x, "impl")$getOutput(name)
  
  [ FAIL 8 | WARN 433 | SKIP 8 | PASS 1331 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'sysfonts', 'showtextdb'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Package suggested but not available for checking: ‘edgeR’
Error(s) in re-building vignettes:
--- re-building ‘MoosePopR-SightabilityPopR-Demo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
New names:
* `Lone Cows` -> Lone.Cows
* `Cow W/1 \r\ncalf` -> Cow.W.1...calf
* `Cow W/2 calves` -> Cow.W.2.calves
* `Lone \r\ncalf` -> Lone...calf
* `Unk Age/Sex` -> Unk.Age.Sex
* ...
Quitting from lines 139-151 (MoosePopR-SightabilityPopR-Demo.Rmd) 
Error: processing vignette 'MoosePopR-SightabilityPopR-Demo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘MoosePopR-SightabilityPopR-Demo.Rmd’

--- re-building ‘RatioEstimator.pdf.asis’ using asis
--- finished re-building ‘RatioEstimator.pdf.asis’

--- re-building ‘SightabilityModel.Rnw’ using Sweave
--- finished re-building 'SightabilityModel.Rnw'

SUMMARY: processing the following file failed:
  ‘MoosePopR-SightabilityPopR-Demo.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘getting-started.Rmd’

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

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

Packages suggested but not available for checking:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19', 'GenomicRanges',
  'copynumber'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘sigmoid.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-67 (sigmoid.Rmd) 
Error: processing vignette 'sigmoid.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sigmoid.Rmd’

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

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

Packages suggested but not available for checking:
  'chromVAR', 'SummarizedExperiment', 'TFBSTools', 'motifmatchr',
  'BSgenome', 'rtracklayer', 'biovizBase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Packages required but not available: 'survcomp', 'GSVA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘signs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 40-74 (signs.Rmd) 
Error: processing vignette 'signs.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘signs.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ComplexHeatmap', 'RankProd', 'GSVA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘siland.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 79-89 (siland.Rmd) 
Error: processing vignette 'siland.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘siland.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simulation_arguments.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 111-116 (simulation_arguments.Rmd) 
Error: processing vignette 'simulation_arguments.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘simulation_arguments.Rmd’

--- re-building ‘tidy_simulation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tidy_simulation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_ITS_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 34-46 (simple_ITS_example.Rmd) 
Error: processing vignette 'simple_ITS_example.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘simple_ITS_example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Error(s) in re-building vignettes:
--- re-building ‘plot.simmer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'simmer.plot'

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

    get_mon_arrivals, get_mon_attributes, get_mon_resources

Quitting from lines 72-76 (plot.simmer.Rmd) 
Error: processing vignette 'plot.simmer.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘plot.simmer.Rmd’

--- re-building ‘plot.trajectory.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘plot.trajectory.Rmd’

SUMMARY: processing the following file failed:
  ‘plot.simmer.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  13.8Mb
Packages required but not available: 'BSgenome', 'GenomicRanges'

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’

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

Package suggested but not available for checking: ‘clipper’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      find
  
  The following objects are masked from 'package:base':
  
      remove, serialize
  
  > 
  > test_check("simplextree")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_simplex_tree.R:508:3): plotting is silent ─────────────────────
  `plot(st)` produced warnings.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 256 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘intro_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 57-60 (intro_vignette.Rmd) 
Error: processing vignette 'intro_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro_vignette.Rmd’

--- re-building ‘reanalysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.3     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   2.0.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 42-43 (reanalysis.Rmd) 
Error: processing vignette 'reanalysis.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘reanalysis.Rmd’

SUMMARY: processing the following files failed:
  ‘intro_vignette.Rmd’ ‘reanalysis.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.7Mb
Package required but not available: ‘ShortRead’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘simrec-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 155-198 (simrec-vignette.Rmd) 
Error: processing vignette 'simrec-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘simrec-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SimRVSequences.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 694-700 (SimRVSequences.Rmd) 
Error: processing vignette 'SimRVSequences.Rmd' failed with diagnostics:
Labels leave no room for the graph, reduce cex
--- failed re-building ‘SimRVSequences.Rmd’

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

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

> ### Name: sims_check
> ### Title: Check Simulated Data
> ### Aliases: sims_check
> 
> ### ** Examples
> 
> set.seed(10)
> sims_simulate("a ~ dunif(0,1)",
+   save = TRUE, path = tempdir(), exists = NA,
+   ask = FALSE
+ )
Error: Package 'rjags' must be installed to simulate data using JAGS code.
Backtrace:
    █
 1. └─sims::sims_simulate(...)
 2.   └─sims:::generate_datasets(...)
 3.     └─chk::err("Package 'rjags' must be installed to simulate data using JAGS code.")
 4.       └─rlang::exec(abort, msg, .subclass = .subclass, !!!args[named])
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   3.     └─chk::err("Package 'rjags' must be installed to simulate data using JAGS code.")
   4.       └─rlang::exec(abort, msg, .subclass = .subclass, !!!args[named])
  ── Error (test-simulate.R:1131:3): progress ────────────────────────────────────
  Error: Package 'rjags' must be installed to simulate data using JAGS code.
  Backtrace:
      █
   1. ├─progressr::with_progress(...) test-simulate.R:1131:2
   2. └─sims::sims_simulate("a ~ dunif(0,1)", nsims = 1L)
   3.   └─sims:::generate_datasets(...)
   4.     └─chk::err("Package 'rjags' must be installed to simulate data using JAGS code.")
   5.       └─rlang::exec(abort, msg, .subclass = .subclass, !!!args[named])
  
  [ FAIL 36 | WARN 0 | SKIP 1 | PASS 70 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sims.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-27 (sims.Rmd) 
Error: processing vignette 'sims.Rmd' failed with diagnostics:
Package 'rjags' must be installed to simulate data using JAGS code.
--- failed re-building ‘sims.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simstandard_tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 115-117 (simstandard_tutorial.Rmd) 
Error: processing vignette 'simstandard_tutorial.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘simstandard_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  26.0Mb
Packages suggested but not available for checking:
  'SummarizedExperiment', 'SingleCellExperiment'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/SiteAdapt.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘big_crush_test.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘big_crush_test.Rmd’

--- re-building ‘sitmo_internals.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sitmo_internals.Rmd’

--- re-building ‘uniform_rng_with_sitmo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 159-163 (uniform_rng_with_sitmo.Rmd) 
Error: processing vignette 'uniform_rng_with_sitmo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘uniform_rng_with_sitmo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TestEquations.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 231-242 (TestEquations.Rmd) 
Error: processing vignette 'TestEquations.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘TestEquations.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/sjdbc.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.1Mb
installed size is 38.6Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SK.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 67-71 (SK.Rmd) 
Error: processing vignette 'SK.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘SK.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘skynet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'kableExtra'

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

    group_rows

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

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

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

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 97-101 (skynet.Rmd) 
Error: processing vignette 'skynet.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘skynet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘meristems.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 49-50 (meristems.Rmd) 
Error: processing vignette 'meristems.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘meristems.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘slim.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 65-69 (slim.Rmd) 
Error: processing vignette 'slim.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘slim.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [9s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   10. │ ├─graphics::plot(x, ...) setup.R:5:2
   11. │ └─lattice:::plot.trellis(x, ...)
   12. │   └─grid::pushViewport(...)
   13. │     └─base::lapply(vps, push.vp, recording)
   14. │       ├─grid:::FUN(X[[i]], ...)
   15. │       └─grid:::push.vp.viewport(X[[i]], ...)
   16. │         └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   17. └─(function (x) ...
   18.   ├─grid::widthDetails(x)
   19.   └─grid:::widthDetails.text(x)
   20.     └─grid:::grid.Call(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 90 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 85-86 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

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

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

> ### Name: rbind_rakelist
> ### Title: rbind a rakelist
> ### Aliases: rbind_rakelist
> 
> ### ** Examples
> 
> rakelist <- slowrake(txt = dog_pubs$abstract[1:2])

  |                                                                            
  |                                                                      |   0%
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(slowraker)
  > 
  > test_check("slowraker")
  
    |                                                                            
    |                                                                      |   0%
Error(s) in re-building vignettes:
  ...
--- re-building ‘faqs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘faqs.Rmd’

sh: line 1: 69421 Trace/BPT trap: 5       '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpkBqehR/file10e7514f1b42e' 2>&1 < '/Volumes/Temp/tmp/RtmpkBqehR/file10e7586c42c0'
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'rjags', 'gWidgets2RGtk2'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.7Mb
    libs  12.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘make_a_social_media_plot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 41-42 (make_a_social_media_plot.Rmd) 
Error: processing vignette 'make_a_social_media_plot.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘make_a_social_media_plot.Rmd’

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

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

> ### Name: sm.surface3d
> ### Title: Adding a regression surface to an rgl plot.
> ### Aliases: sm.surface3d
> ### Keywords: nonparametric regression smooth
> 
> ### ** Examples
> 
> with(trawl, {
+    Zone93    <- (Year == 1 & Zone == 1)
+    Position  <- cbind(Longitude - 143, Latitude)
+    model1 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.1, 0.1), display = "rgl", xlab="Longitude - 143")
+    model2 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.2, 0.2), display = "none")
+    sm.surface3d(model2$eval.points, model2$est, model1$scaling, col = "red")
+ })
Error in sm.surface3d(model2$eval.points, model2$est, model1$scaling,  : 
  a scaling must be specified.
Calls: with -> with.default -> eval -> eval -> sm.surface3d
Execution halted
Package required but not available: ‘BiocStyle’

Package suggested but not available for checking: ‘biomaRt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      3.3Mb
Error(s) in re-building vignettes:
--- re-building ‘sobir-getstarted.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

`geom_smooth()` using formula 'y ~ x'
Quitting from lines 75-88 (sobir-getstarted.Rmd) 
Error: processing vignette 'sobir-getstarted.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sobir-getstarted.Rmd’

SUMMARY: processing the following file failed:
  ‘sobir-getstarted.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 163-167 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

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

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

> ### Name: fitsoilwater
> ### Title: Interactive Estimation of van Genuchten's (1980) Model
> ###   Parameters
> ### Aliases: fitsoilwater
> 
> ### ** Examples
> 
> # Liu et al. (2011)
> h <- c(0.001, 50.65, 293.77, 790.14, 992.74, 5065, 10130, 15195)
> w <- c(0.5650, 0.4013, 0.2502, 0.2324, 0.2307, 0.1926, 0.1812, 0.1730)
> fitsoilwater(w, h)
Error in fitsoilwater(w, h) : package rpanel is required
Execution halted
Errors in running code in vignettes:
when running code in ‘ParameterEstimation.Rnw’
  ...

> cov0 <- summary(Fit)$cov.scaled

> MCMC <- modMCMC(f = R14tCost, p = Fit$par, niter = 1000, 
+     jump = NULL, var0 = var0, wvar0 = 0, lower = c(-3, -3, -1, 
+         0, 0), upper = .... [TRUNCATED] 

  When sourcing ‘ParameterEstimation.R’:
Error: values of 'p' should be inbetween 'lower' and 'upper'
Execution halted

  ‘GeneralModel.Rnw’... [1s/1s] OK
  ‘ParameterEstimation.Rnw’... failed
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    2.2Mb
    libs   8.2Mb
Error(s) in re-building vignettes:
--- re-building ‘sorvi_tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
sorvi - Tools for Finnish Open Data.
Copyright (C) 2010-2015 Leo Lahti, Juuso Parkkinen, Juuso Haapanen, Einari Happonen, Jussi Paananen, Joona Lehtomaki ym.

http://github.com/ropengov/sorvi 

 Hard sciences are successful because they deal with soft problems; 
 soft sciences are struggling because they deal with hard problems.
-                        Von Foerster

Computing boostrapped smoothers ...
convert bootstrapped spaghettis to long format
Computing density estimates for each vertical cut ...
vertical cross-sectional density estimate
Tile approach
Build ggplot figure ...
Quitting from lines 241-245 (sorvi_tutorial.Rmd) 
Error: processing vignette 'sorvi_tutorial.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sorvi_tutorial.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sos.Rnw’ using Sweave
Loading required package: brew

Attaching package: 'sos'

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

    ?

Warning in readLines(f) :
  incomplete final line found on '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/mdsOpt/INDEX'
Warning in readLines(f) :
  incomplete final line found on '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/cosso/INDEX'

Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘pbmcTutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 168-177 (pbmcTutorial.Rmd) 
Error: processing vignette 'pbmcTutorial.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘pbmcTutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.5Mb
Package required but not available: ‘gRbase’

Packages suggested but not available for checking:
  'r2cytoscape', 'BiocStyle', 'graphite', 'hgu95av2.db', 'ALL',
  'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.4Mb
installed size is 40.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  37.7Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘spatial_multivariate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 107-137 (spatial_multivariate.Rmd) 
Error: processing vignette 'spatial_multivariate.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘spatial_multivariate.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_sparkline.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘intro_sparkline.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    java   3.3Mb
Package suggested but not available for checking: ‘RCy3’
Package unavailable to check Rd xrefs: ‘RCy3’
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 54-55 (using.Rmd) 
Error: processing vignette 'using.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘using.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Starting.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 52-54 (Starting.Rmd) 
Error: processing vignette 'Starting.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Starting.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SBSS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 147-148 (SBSS.Rmd) 
Error: processing vignette 'SBSS.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘SBSS.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    help   1.7Mb
    libs   1.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘spatialsample.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 103-112 (spatialsample.Rmd) 
Error: processing vignette 'spatialsample.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘spatialsample.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 63-73 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  15.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    help   3.9Mb
    libs   1.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    help   2.6Mb
Package required but not available: ‘rpanel’

Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.core', 'spatstat.linnet', 'spatstat.data',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs  28.7Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs  11.9Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.1Mb
    etc   1.3Mb
Error(s) in re-building vignettes:
--- re-building ‘spdplyr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: sp
Checking rgeos availability: TRUE
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 31-37 (spdplyr.Rmd) 
Error: processing vignette 'spdplyr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘spdplyr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘praat-plot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘praat-plot.Rmd’

--- re-building ‘run-praat.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 142-152 (run-praat.Rmd) 
Error: processing vignette 'run-praat.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘run-praat.Rmd’

SUMMARY: processing the following file failed:
  ‘run-praat.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'speaq', 'genefilter', 'specmine.datasets'

Packages suggested but not available for checking:
  'MAIT', 'xcms', 'KEGGgraph', 'rcytoscapejs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.7Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Error(s) in re-building vignettes:
--- re-building ‘getting_started_with_spectre.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Quitting from lines 102-107 (getting_started_with_spectre.Rmd) 
Error: processing vignette 'getting_started_with_spectre.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘getting_started_with_spectre.Rmd’

--- re-building ‘minimal_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Quitting from lines 89-94 (minimal_example.Rmd) 
Error: processing vignette 'minimal_example.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘minimal_example.Rmd’

SUMMARY: processing the following files failed:
  ‘getting_started_with_spectre.Rmd’ ‘minimal_example.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Spectrum_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 68-70 (Spectrum_vignette.Rmd) 
Error: processing vignette 'Spectrum_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Spectrum_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘spind_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-76 (spind_vignette.Rmd) 
Error: processing vignette 'spind_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘spind_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘spiR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 112-114 (spiR.Rmd) 
Error: processing vignette 'spiR.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘spiR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘antaresViz’
Package unavailable to check Rd xrefs: ‘antaresViz’
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      4.5Mb
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `"one joule (Omega\n) ~ 1 kg*m^2./s^2" %>% render` produced warnings.
  ── Failure (test-spork.R:467:3): newline renders sensibly as plotmath ──────────
  `"one joule (\nOmega) ~ 1 kg*m^2./s^2" %>% render` produced warnings.
  ── Failure (test-spork.R:468:3): newline renders sensibly as plotmath ──────────
  `"one joule \n(Omega) ~ 1 kg*m^2./s^2" %>% render` produced warnings.
  ── Failure (test-spork.R:469:3): newline renders sensibly as plotmath ──────────
  `"one joule\n (Omega) ~ 1 kg*m^2./s^2" %>% render` produced warnings.
  ── Failure (test-spork.R:470:3): newline renders sensibly as plotmath ──────────
  `"one \njoule (Omega) ~ 1 kg*m^2./s^2" %>% render` produced warnings.
  ── Failure (test-spork.R:471:3): newline renders sensibly as plotmath ──────────
  `"\none joule (Omega) ~ 1 kg*m^2./s^2" %>% render` produced warnings.
  
  [ FAIL 20 | WARN 0 | SKIP 4 | PASS 79 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sport_in_r.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 105-107 (sport_in_r.Rmd) 
Error: processing vignette 'sport_in_r.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sport_in_r.Rmd’

--- re-building ‘the_theory.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘the_theory.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Clustering-hot-spots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 299-305 (Clustering-hot-spots.Rmd) 
Error: processing vignette 'Clustering-hot-spots.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Clustering-hot-spots.Rmd’

SUMMARY: processing the following file failed:
  ‘Clustering-hot-spots.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 59.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  57.9Mb
Error(s) in re-building vignettes:
--- re-building ‘spsurv.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: survival
Loading required package: loo
This is loo version 2.4.1
- Online documentation and vignettes at mc-stan.org/loo
- As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. 
Loading required package: coda
Loading required package: MASS

Attaching package: 'spsurv'

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

    traceplot

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

    coef, confint, vcov

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

    mode

Priors are ignored due to mle approach.
Priors are ignored due to mle approach.
Quitting from lines 125-127 (spsurv.Rmd) 
Error: processing vignette 'spsurv.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘spsurv.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sptotal-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Quitting from lines 153-157 (sptotal-vignette.Rmd) 
Error: processing vignette 'sptotal-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sptotal-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/SqlRender.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘RODBC’
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
File ‘sqp/libs/sqp.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
    Object: ‘solver_dense.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘extending-srvyr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘extending-srvyr.Rmd’

--- re-building ‘srvyr-database.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘srvyr-database.Rmd’

--- re-building ‘srvyr-vs-survey.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

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

    dotchart


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

`summarise()` has grouped output by 'stype'. You can override using the `.groups` argument.
Quitting from lines 31-47 (srvyr-vs-survey.Rmd) 
Error: processing vignette 'srvyr-vs-survey.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘srvyr-vs-survey.Rmd’

SUMMARY: processing the following file failed:
  ‘srvyr-vs-survey.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 379-386 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

--- re-building ‘making-models.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘making-models.Rmd’

--- re-building ‘modifying-models.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘modifying-models.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 97.9Mb
  sub-directories of 1Mb or more:
    libs  97.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘stabm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required namespace: ggplot2
Loading required namespace: cowplot
Loading required namespace: ggdendro
Quitting from lines 65-66 (stabm.Rmd) 
Error: processing vignette 'stabm.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘stabm.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    include  10.2Mb
    lib       2.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/staplr.Rcheck/00install.out’ for details.
Packages required but not available:
  'RGtk2', 'gWidgets2RGtk2', 'cairoDevice', 'RSCABS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   6.0Mb
Running ‘tinytest.R’ [3s/3s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  test_plots.R..................   29 tests [0;32mOK[0m 
  test_plots.R..................   30 tests [0;32mOK[0m 
  test_plots.R..................   31 tests [0;32mOK[0m 
  test_plots.R..................   32 tests [0;32mOK[0m 
  test_plots.R..................   33 tests [0;31m1 fails[0m 
  test_plots.R..................   34 tests [0;31m1 fails[0m 
  test_plots.R..................   35 tests [0;31m1 fails[0m 
  test_plots.R..................   36 tests [0;31m1 fails[0m 
  test_plots.R..................   37 tests [0;31m1 fails[0m 
  test_plots.R..................   38 tests [0;31m1 fails[0m 
  test_plots.R..................   38 tests [0;31m1 fails[0m Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  : 
    polygon edge not found
  Calls: <Anonymous> ... <Anonymous> -> widthDetails -> widthDetails.text -> grid.Call
  In addition: There were 50 or more warnings (use warnings() to see the first 50)
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GWAS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 245-247 (GWAS.Rmd) 
Error: processing vignette 'GWAS.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘GWAS.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘statgenGxE.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 71-76 (statgenGxE.Rmd) 
Error: processing vignette 'statgenGxE.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘statgenGxE.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘tinytest.R’ [31s/31s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  ----- FAILED[data]: test_utils.R<94--95>
   call| expect_equal((statgenHTP:::prettier(n = 1))(times), strptime("21sep2019 12:00", 
   call| -->    "%d%b%Y %H:%M"))
   diff| Mean absolute difference: 1800
  ----- FAILED[data]: test_utils.R<96--97>
   call| expect_equal((statgenHTP:::prettier(n = 2))(times), strptime(c("9sep2019 12:00", 
   call| -->    "3oct2019 12:00"), "%d%b%Y %H:%M"))
   diff| Mean absolute difference: 720
  ----- FAILED[data]: test_utils.R<98--100>
   call| expect_equal((statgenHTP:::prettier(n = 3))(times), strptime(c("6sep2019 12:00", 
   call| -->    "21sep2019 12:00", "6oct2019 12:00"), "%d%b%Y %H:%M"))
   diff| Mean absolute difference: 900
  Error: 5 out of 492 tests failed
  In addition: There were 27 warnings (use warnings() to see them)
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview_HTP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 103-107 (Overview_HTP.Rmd) 
Error: processing vignette 'Overview_HTP.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Overview_HTP.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘statgenSTA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 169-171 (statgenSTA.Rmd) 
Error: processing vignette 'statgenSTA.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘statgenSTA.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.5Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Error(s) in re-building vignettes:
--- re-building ‘custom_function_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: sp

Attaching package: 'future'

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

    values

Quitting from lines 93-99 (custom_function_example.Rmd) 
Error: processing vignette 'custom_function_example.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘custom_function_example.Rmd’

--- re-building ‘kangaroo_model_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: sp

Attaching package: 'future'

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

    values

Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Quitting from lines 76-80 (kangaroo_model_example.Rmd) 
Error: processing vignette 'kangaroo_model_example.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘kangaroo_model_example.Rmd’

SUMMARY: processing the following files failed:
  ‘custom_function_example.Rmd’ ‘kangaroo_model_example.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.8Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   8.0Mb
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Running ‘testthat.R’ [1s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > # Since the tests are supposed to guarantee that the bundled version installed
  > # correctly, they are skipped.
  > if (!is_solaris()) {
  +   test_check("stockfish")
  + }
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-fish.R:12:3): engine works ────────────────────────────────────
  engine$isready() is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘strand.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 471-472 (strand.Rmd) 
Error: processing vignette 'strand.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘strand.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-streamDepletr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 71-81 (intro-to-streamDepletr.Rmd) 
Error: processing vignette 'intro-to-streamDepletr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro-to-streamDepletr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/streamMOA.Rcheck/00install.out’ for details.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  12.5Mb
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    libs  31.7Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9. │               └─waldo:::ses(x, y, elementwise = elementwise)
   10. └─base::loadNamespace(x)
   11.   ├─base::namespaceImportFrom(...)
   12.   │ └─base::asNamespace(ns)
   13.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   14.     ├─base::namespaceImportFrom(...)
   15.     │ └─base::asNamespace(ns)
   16.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   17.       └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   18.         └─base:::withOneRestart(expr, restarts[[1L]])
   19.           └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 216 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘ShortRead’

Package suggested but not available for checking: ‘STRaitRazoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘package_functions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 81-103 (package_functions.Rmd) 
Error: processing vignette 'package_functions.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘package_functions.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/subspace.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘plotting_functions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'https://www.uniklinik-freiburg.de/fileadmin/mediapool/08_institute/biometrie-statistik/Dateien/Studium_und_Lehre/Lehrbuecher/Multivariable_Model-building/adv_prostate_ca.zip'
Content type 'application/zip' length 62590 bytes (61 KB)
==================================================
downloaded 61 KB

Quitting from lines 76-81 (plotting_functions.Rmd) 
Error: processing vignette 'plotting_functions.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘plotting_functions.Rmd’

--- re-building ‘subbuild_function.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'https://www.uniklinik-freiburg.de/fileadmin/mediapool/08_institute/biometrie-statistik/Dateien/Studium_und_Lehre/Lehrbuecher/Multivariable_Model-building/adv_prostate_ca.zip'
Content type 'application/zip' length 62590 bytes (61 KB)
==================================================
downloaded 61 KB

--- finished re-building ‘subbuild_function.Rmd’

--- re-building ‘subtee_package.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'https://www.uniklinik-freiburg.de/fileadmin/mediapool/08_institute/biometrie-statistik/Dateien/Studium_und_Lehre/Lehrbuecher/Multivariable_Model-building/adv_prostate_ca.zip'
Content type 'application/zip' length 62590 bytes (61 KB)
==================================================
downloaded 61 KB

--- finished re-building ‘subtee_package.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘shinygains.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘shinygains.Rmd’

--- re-building ‘suddengains-tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 597-599 (suddengains-tutorial.Rmd) 
Error: processing vignette 'suddengains-tutorial.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘suddengains-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘suddengains-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Tasmania.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

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

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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Error(s) in re-building vignettes:
  ...
--- re-building ‘pipeline.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Quitting from lines 171-183 (pipeline.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Error(s) in re-building vignettes:
  ...
--- re-building ‘set_html.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Quitting from lines 115-116 (set_html.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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Packages suggested but not available for checking: 'genefilter', 'sva'
Running examples in ‘SuperLearner-Ex.R’ failed
The error most likely occurred in:

> ### Name: SL.extraTrees
> ### Title: extraTrees SuperLearner wrapper
> ### Aliases: SL.extraTrees
> 
> ### ** Examples
> 
> 
> data(Boston, package = "MASS")
> Y = Boston$medv
> # Remove outcome from covariate dataframe.
> X = Boston[, -14]
> 
> set.seed(1)
> 
> # Sample rows to speed up example.
> row_subset = sample(nrow(X), 30)
> 
> sl = SuperLearner(Y[row_subset], X[row_subset, ], family = gaussian(),
+ cvControl = list(V = 2), SL.library = c("SL.mean", "SL.extraTrees"))
Loading required namespace: extraTrees
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Package created on 2021-05-04
  
  > 
  > test_check("SuperLearner")
  
  Call:  
  SuperLearner(Y = Y_reg, X = X, family = gaussian(), SL.library = c(SL.library,  
      xgb_grid$names), cvControl = list(V = 2)) 
  
  
                     Risk        Coef
  SL.mean_All    1.100027 0.695294753
  SL.xgboost_All 1.532526 0.006625806
  SL.xgb.1_All   1.593716 0.298079441
  SL.xgb.2_All   1.642955 0.000000000
installed size is  6.8Mb
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Packages suggested but not available for checking: 'INLA', 'runjags'
installed size is  8.8Mb
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    R      2.1Mb
    doc    2.4Mb
    libs   1.9Mb
Package unavailable to check Rd xrefs: ‘runjags’
Running examples in ‘surveillance-Ex.R’ failed
The error most likely occurred in:

> ### Name: sts_animate
> ### Title: Animated Maps and Time Series of Disease Counts or Incidence
> ### Aliases: animate.sts
> ### Keywords: hplot dynamic spatial
> 
> ### ** Examples
> 
> data("measlesWeserEms")
> 
> ## animate the weekly counts of measles (during weeks 12-16 only, for speed)
> if (require("animation")) {
+     oldwd <- setwd(tempdir())  # to not clutter up the current working dir
+     saveHTML(animate(measlesWeserEms, tps=12:16),
+              title="Evolution of the measles epidemic in the Weser-Ems region",
+              ani.width=500, ani.height=600)
+     setwd(oldwd)
+ }
Loading required package: animation
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  : 
  polygon edge not found
Calls: saveHTML ... <Anonymous> -> widthDetails -> widthDetails.text -> grid.Call
Execution halted
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Error(s) in re-building vignettes:
--- re-building ‘multivariate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.3     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   2.0.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 88-89 (multivariate.Rmd) 
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--- re-building ‘univariate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.3     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   2.0.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 104-105 (univariate.Rmd) 
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SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted
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Package unavailable to check Rd xrefs: ‘survJamda’
Package required but not available: ‘survcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘survParamSim.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Quitting from lines 53-58 (survParamSim.Rmd) 
Error: processing vignette 'survParamSim.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error(s) in re-building vignettes:
  ...
--- re-building ‘survtmle_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 547-549 (survtmle_intro.Rmd) 
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SUMMARY: processing the following file failed:
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Error(s) in re-building vignettes:
  ...
--- re-building ‘Svplots_and_Testing_Hypothes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Quitting from lines 39-42 (Svplots_and_Testing_Hypothes.Rmd) 
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.to.swimplot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Quitting from lines 63-64 (Introduction.to.swimplot.Rmd) 
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--- re-building ‘Using.swimplot.to.display.toxicity.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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SUMMARY: processing the following files failed:
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  ‘Using.swimplot.to.display.toxicity.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'cplexAPI', 'clpAPI'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/symengine.Rcheck/00install.out’ for details.
installed size is  5.7Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/sysfonts.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘systemfit.Rnw’ using Sweave
Loading required package: Matrix
Loading required package: car
Loading required package: carData
Loading required package: lmtest
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric


Please cite the 'systemfit' package as:
Arne Henningsen and Jeff D. Hamann (2007). systemfit: A Package for Estimating Systems of Simultaneous Equations in R. Journal of Statistical Software 23(4), 1-40. http://www.jstatsoft.org/v23/i04/.

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

Error: processing vignette 'systemfit.Rnw' failed with diagnostics:
 chunk 43 (label = systemfit_sem) 
Error : package or namespace load failed for ‘sem’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘mi’

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

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Error(s) in re-building vignettes:
--- re-building ‘table1-examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Attaching package: 'table1'

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

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--- re-building ‘table1-latex.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Attaching package: 'flextable'

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

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Attaching package: 'table1'

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

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--- finished re-building ‘table1-latex.Rmd’

SUMMARY: processing the following file failed:
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Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/table1xls.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘bibliography.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘bibliography.Rmd’

--- re-building ‘diversity.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Quitting from lines 340-353 (diversity.Rmd) 
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--- re-building ‘seriation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/tabulizerjars.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/tabulizer.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    7. │ ├─base::plot(x, ...)
    8. │ └─lattice:::plot.trellis(x, ...)
    9. │   └─grid::pushViewport(...)
   10. │     └─base::lapply(vps, push.vp, recording)
   11. │       ├─grid:::FUN(X[[i]], ...)
   12. │       └─grid:::push.vp.viewport(X[[i]], ...)
   13. │         └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   14. └─(function (x) ...
   15.   ├─grid::widthDetails(x)
   16.   └─grid:::widthDetails.text(x)
   17.     └─grid:::grid.Call(...)
  
  [ FAIL 3 | WARN 44 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tagcloud.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
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Error(s) in re-building vignettes:
  ...
--- re-building ‘available_templates.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Error(s) in re-building vignettes:
--- re-building ‘tbm_supplement.Rnw’ using knitr
Loading required package: mlt
Loading required package: basefun
Loading required package: variables
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
Loading required package: grid

Attaching package: 'grid'

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

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Loading required package: libcoin
Loading required package: mvtnorm

Attaching package: 'partykit'

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

    varimp

Warning in ngradient(y, fit, weights) :
  risk increase; decrease stepsize nu

warning: solve(): system is singular (rcond: 1.47925e-21); attempting approx solution

warning: solve(): system is singular (rcond: 1.47925e-21); attempting approx solution
Warning in ngradient(y, fit, weights) :
  risk increase; decrease stepsize nu
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
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Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_tbrf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
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Error(s) in re-building vignettes:
  ...
--- re-building ‘testarguments.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 114-115 (testarguments.Rmd) 
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--- re-building ‘GIAValidationExample.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Package suggested but not available for checking: ‘usethis’
installed size is  9.0Mb
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Package required but not available: ‘minet’

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

> ### Name: tgs_graph_cover_resample
> ### Title: Clusters directed graph multiple times with randomized sample
> ###   subset
> ### Aliases: tgs_graph_cover_resample
> ### Keywords: ~cluster
> 
> ### ** Examples
> 
> 
> ## Don't show: 
> set.seed(seed = 0)
> rows <- 100
> cols <- 200
> vals <- sample(1 : (rows * cols / 2), rows * cols, replace = TRUE)
> m <- matrix(vals, nrow = rows, ncol = cols)
> 
> r1 <- tgs_cor(m, pairwise.complete.obs = FALSE, spearman = TRUE)
> r2 <- tgs_knn(r1, knn = 20, diag = FALSE)
> r3 <- tgs_graph(r2, knn = 3, k_expand = 10)
> r4 <- tgs_graph_cover_resample(r3, 10, 1, n_resamp = 5)
Error: Child process 69620 ended unexpectedly
Execution halted
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Packages suggested but not available for checking:
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Packages unavailable to check Rd xrefs: ‘runjags’, ‘rjags’, ‘jagsUI’
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

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

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Quitting from lines 88-101 (intro.Rmd) 
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Error(s) in re-building vignettes:
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--- re-building ‘tidydice.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

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Quitting from lines 147-150 (tidydice.Rmd) 
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Error: Vignette re-building failed.
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Error(s) in re-building vignettes:
  ...
--- re-building ‘using-tidyestimate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 81-82 (using-tidyestimate.Rmd) 
Error: processing vignette 'using-tidyestimate.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘using-tidyestimate.Rmd’

SUMMARY: processing the following file failed:
  ‘using-tidyestimate.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 113-154 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_tidyLPA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
You can use the function citation('tidyLPA') to create a citation for the use of {tidyLPA}.
Mplus is not installed. Use only package = 'mclust' when calling estimate_profiles().

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 115-121 (Introduction_to_tidyLPA.Rmd) 
Error: processing vignette 'Introduction_to_tidyLPA.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction_to_tidyLPA.Rmd’

--- re-building ‘benchmarking-mclust-and-mplus.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘benchmarking-mclust-and-mplus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TidyMultiqc.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 74-77 (TidyMultiqc.Rmd) 
Error: processing vignette 'TidyMultiqc.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘TidyMultiqc.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plot-smooths.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 60-66 (plot-smooths.Rmd) 
Error: processing vignette 'plot-smooths.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘plot-smooths.Rmd’

--- re-building ‘predict-gam.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 75-78 (predict-gam.Rmd) 
Error: processing vignette 'predict-gam.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘predict-gam.Rmd’

SUMMARY: processing the following files failed:
  ‘plot-smooths.Rmd’ ‘predict-gam.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Package unavailable to check Rd xrefs: ‘Rblpapi’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
--- finished re-building ‘introduction.Rmd’

--- re-building ‘servicepatterns.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 116-121 (servicepatterns.Rmd) 
Error: processing vignette 'servicepatterns.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘servicepatterns.Rmd’

--- re-building ‘timetable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 180-192 (timetable.Rmd) 
Error: processing vignette 'timetable.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘timetable.Rmd’

SUMMARY: processing the following files failed:
  ‘servicepatterns.Rmd’ ‘timetable.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘use-tidytreatment-BART.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 163-177 (use-tidytreatment-BART.Rmd) 
Error: processing vignette 'use-tidytreatment-BART.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘use-tidytreatment-BART.Rmd’

SUMMARY: processing the following file failed:
  ‘use-tidytreatment-BART.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_tidyusda.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 72-89 (using_tidyusda.Rmd) 
Error: processing vignette 'using_tidyusda.Rmd' failed with diagnostics:
lexical error: invalid char in json text.
                                       <!DOCTYPE html PUBLIC "-//W3C//
                     (right here) ------^

--- failed re-building ‘using_tidyusda.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘tidyvpc.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: data.table
Loading required package: magrittr
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve

Warning in rq.fit.sfn(x, y, tau = tau, rhs = rhs, control = control, ...) :
  tiny diagonals replaced with Inf when calling blkfct

Warning in rq.fit.sfn(x, y, tau = tau, rhs = rhs, control = control, ...) :
  tiny diagonals replaced with Inf when calling blkfct

Quitting from lines 180-186 (tidyvpc.Rmd) 
Error: processing vignette 'tidyvpc.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘tidyvpc.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘data-validation-rules.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘data-validation-rules.Rmd’

--- re-building ‘smells.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 141-157 (smells.Rmd) 
Error: processing vignette 'smells.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘smells.Rmd’

--- re-building ‘tidyxl.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tidyxl.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 29.5Mb
  sub-directories of 1Mb or more:
    libs    13.0Mb
    tiledb  14.6Mb
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   31. |     \-grid::pushViewport(vp, recording = FALSE)
   32. |       \-base::lapply(vps, push.vp, recording)
   33. |         +-grid:::FUN(X[[i]], ...)
   34. |         \-grid:::push.vp.vpTree(X[[i]], ...)
   35. |           +-grid:::push.vp(vp$parent, recording)
   36. |           \-grid:::push.vp.viewport(vp$parent, recording)
   37. |             \-grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   38. \-(function (x) ...
   39.   +-grid::widthDetails(x)
   40.   \-grid:::widthDetails.text(x)
   41.     \-grid:::grid.Call(...)
  
  [ FAIL 1 | WARN 3 | SKIP 1 | PASS 18 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plot_timeline.Rmd’ using knitr
Quitting from lines 51-53 (plot_timeline.Rmd) 
Error: processing vignette 'plot_timeline.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building 'plot_timeline.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tintHtmlIntro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-53 (tintHtmlIntro.Rmd) 
Error: processing vignette 'tintHtmlIntro.Rmd' failed with diagnostics:
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--- failed re-building ‘tintHtmlIntro.Rmd’

--- re-building ‘tintPdfIntro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-52 (tintPdfIntro.Rmd) 
Error: processing vignette 'tintPdfIntro.Rmd' failed with diagnostics:
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--- failed re-building ‘tintPdfIntro.Rmd’

SUMMARY: processing the following files failed:
  ‘tintHtmlIntro.Rmd’ ‘tintPdfIntro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tinyscholar.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 89-92 (tinyscholar.Rmd) 
Error: processing vignette 'tinyscholar.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘tinyscholar.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Error(s) in re-building vignettes:
--- re-building ‘comparison_of_computation_time.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Rcpp

Attaching package: 'lmom'

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

    cdfexp, cdfgam, cdfgev, cdfglo, cdfgno, cdfgpa, cdfgum, cdfkap,
    cdfln3, cdfnor, cdfpe3, cdfwak, cdfwei, quaexp, quagam, quagev,
    quaglo, quagno, quagpa, quagum, quakap, qualn3, quanor, quape3,
    quawak, quawei

--- finished re-building ‘comparison_of_computation_time.Rmd’

--- re-building ‘short_introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 152-156 (short_introduction.Rmd) 
Error: processing vignette 'short_introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘short_introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    examples  12.0Mb
    include    2.9Mb
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs  34.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/tm.plugin.webmining.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘Rpoppler’
Error(s) in re-building vignettes:
--- re-building ‘polling_districts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 44-79 (polling_districts.Rmd) 
Error: processing vignette 'polling_districts.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘polling_districts.Rmd’

--- re-building ‘tongfen-ca-estimate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tongfen-ca-estimate.Rmd’

--- re-building ‘tongfen.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tongfen.Rmd’

--- re-building ‘tongfen_ca.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tongfen_ca.Rmd’

--- re-building ‘tongfen_us.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tongfen_us.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 223.5Mb
  sub-directories of 1Mb or more:
    R       5.1Mb
    help    1.4Mb
    libs  216.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘demo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 76-82 (demo.Rmd) 
Error: processing vignette 'demo.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Quitting from lines 86-87 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
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--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Loading required package: splines
Loading required package: Matrix
Loading required package: fds
Loading required package: rainbow
Loading required package: MASS
Loading required package: pcaPP
Loading required package: RCurl

Attaching package: 'fda'

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

    matplot

--- finished re-building 'trackeR.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘index.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: histry
--- finished re-building ‘index.Rmd’

--- re-building ‘Extending-trackr.Rnw’ using knitr
Quitting from lines 146-155 (Extending-trackr.Rnw) 
Error: processing vignette 'Extending-trackr.Rnw' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Extending-trackr.Rnw’

SUMMARY: processing the following file failed:
  ‘Extending-trackr.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TrajDataMining.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 49-54 (TrajDataMining.Rmd) 
Error: processing vignette 'TrajDataMining.Rmd' failed with diagnostics:
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--- failed re-building ‘TrajDataMining.Rmd’

SUMMARY: processing the following file failed:
  ‘TrajDataMining.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 52.3Mb
  sub-directories of 1Mb or more:
    libs  50.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Package required but not available: ‘phyloseq’

Package suggested but not available for checking: ‘adaptiveGPCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘explore.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 33-36 (explore.Rmd) 
Error: processing vignette 'explore.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘explore.Rmd’

SUMMARY: processing the following file failed:
  ‘explore.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-treemapify.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 32-34 (introduction-to-treemapify.Rmd) 
Error: processing vignette 'introduction-to-treemapify.Rmd' failed with diagnostics:
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--- failed re-building ‘introduction-to-treemapify.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction-to-treemapify.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘treemap-color_mapping.Rmd’ using knitr
Quitting from lines 35-36 (treemap-color_mapping.Rmd) 
Error: processing vignette 'treemap-color_mapping.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘treemap-color_mapping.Rmd’

SUMMARY: processing the following file failed:
  ‘treemap-color_mapping.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘structuredCoalescent.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 64-65 (structuredCoalescent.Rmd) 
Error: processing vignette 'structuredCoalescent.Rmd' failed with diagnostics:
"ggtree" %in% utils::installed.packages()[, 1] is not TRUE
--- failed re-building ‘structuredCoalescent.Rmd’

SUMMARY: processing the following file failed:
  ‘structuredCoalescent.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   33. │     └─grid::pushViewport(vp, recording = FALSE)
   34. │       └─base::lapply(vps, push.vp, recording)
   35. │         ├─grid:::FUN(X[[i]], ...)
   36. │         └─grid:::push.vp.vpTree(X[[i]], ...)
   37. │           ├─grid:::push.vp(vp$parent, recording)
   38. │           └─grid:::push.vp.viewport(vp$parent, recording)
   39. │             └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   40. └─(function (x) ...
   41.   ├─grid::widthDetails(x)
   42.   └─grid:::widthDetails.text(x)
   43.     └─grid:::grid.Call(...)
  
  [ FAIL 1 | WARN 45 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘trelliscopejs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 57-60 (trelliscopejs.Rmd) 
Error: processing vignette 'trelliscopejs.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘trelliscopejs.Rmd’

SUMMARY: processing the following file failed:
  ‘trelliscopejs.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘prediction_intervals.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 53-101 (prediction_intervals.Rmd) 
Error: processing vignette 'prediction_intervals.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘prediction_intervals.Rmd’

SUMMARY: processing the following file failed:
  ‘prediction_intervals.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 139.4Mb
  sub-directories of 1Mb or more:
    doc     3.8Mb
    libs  134.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘choropleth_maps_with_tricolore.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 61-72 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘choropleth_maps_with_tricolore.Rmd’

SUMMARY: processing the following file failed:
  ‘choropleth_maps_with_tricolore.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    libs  43.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘trinROC_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 191-230 (trinROC_vignette.Rmd) 
Error: processing vignette 'trinROC_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘trinROC_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘trinROC_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Running ‘testthat.R’ [11s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       █
    1. ├─tsbox::ts_seas(ts_c(mdeaths, fdeaths), x11 = "") test_ts_.R:51:2
    2. │ └─tsbox::ts_apply(x, ff, ...)
    3. │   └─tsbox:::ts_apply_dts(ts_dts(x), fun, ...)
    4. │     ├─x[, fun(.SD, ...), by = eval(.by)]
    5. │     └─data.table:::`[.data.table`(x, , fun(.SD, ...), by = eval(.by))
    6. └─tsbox:::fun(.SD, ...)
    7.   └─(function(x, ...) seasonal::final(seasonal::seas(x, ...)))(...)
    8.     ├─seasonal::final(seasonal::seas(x, ...))
    9.     └─seasonal::seas(x, ...)
   10.       └─seasonal::checkX13(fail = TRUE, fullcheck = FALSE, htmlcheck = FALSE)
  
  [ FAIL 1 | WARN 0 | SKIP 13 | PASS 457 ]
  Error: Test failures
  Execution halted
Package which this enhances but not available for checking: ‘TSodbc’
Packages suggested but not available for checking: 'TSodbc', 'RODBC'
Packages unavailable to check Rd xrefs: ‘TSodbc’, ‘RODBC’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
> options(continue = "  ")

> library("tframe")

> library("tfplot")

> library("TSsdmx")
Loading required package: TSdbi

... incomplete output.  Crash?
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

> user <- Sys.getenv("MYSQL_USER")

> setup <- RMySQL::dbConnect(RMySQL::MySQL(), dbname = "test")

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted

  ‘Guide.Stex’... failed to complete the test
  ‘GuideAppendix.Stex’... failed
  ‘GuideDevel.Stex’... [0s/0s] OK
Error(s) in re-building vignettes:
  ...
sh: line 1: 70169 Trace/BPT trap: 5       '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpMHPXFU/file111ef785602f9' 2>&1 < '/Volumes/Temp/tmp/RtmpMHPXFU/file111ef56dd6727'
--- re-building ‘Guide.Stex’ using Sweave
Loading required package: TSdbi
--- re-building ‘GuideAppendix.Stex’ using Sweave

Error: processing vignette 'GuideAppendix.Stex' failed with diagnostics:
 chunk 3 
Error in .local(drv, ...) : 
  Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)


--- failed re-building ‘GuideAppendix.Stex’

--- re-building ‘GuideDevel.Stex’ using Sweave
--- finished re-building ‘GuideDevel.Stex’

SUMMARY: processing the following files failed:
  ‘Guide.Stex’ ‘GuideAppendix.Stex’

Error: Vignette re-building failed.
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   9.0Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   3.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/TSsdmx.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘fprVSp.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 383-384 (fprVSp.Rmd) 
Error: processing vignette 'fprVSp.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘fprVSp.Rmd’

--- re-building ‘lookDeeper.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘lookDeeper.Rmd’

SUMMARY: processing the following file failed:
  ‘fprVSp.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 41-43 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘example.Rmd’

SUMMARY: processing the following file failed:
  ‘example.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 72-75 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘briefTutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 110-111 (briefTutorial.Rmd) 
Error: processing vignette 'briefTutorial.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘briefTutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘briefTutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘twangRDC.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in ps.xgb(sim_pik ~ c00_age12 + c00_race + c00_sex, strata = "tract_id_str",  :
  Convergence criteria was not achieved. Consider increasing max.steps or iters.per.step.
Quitting from lines 188-189 (twangRDC.Rmd) 
Error: processing vignette 'twangRDC.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘twangRDC.Rmd’

SUMMARY: processing the following file failed:
  ‘twangRDC.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 64.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  61.3Mb
Package required but not available: ‘ChemmineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘api.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 83-84 (api.Rmd) 
Error: processing vignette 'api.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘api.Rmd’

SUMMARY: processing the following file failed:
  ‘api.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       27.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/udunits2.Rcheck/00install.out’ for details.
installed size is 347.7Mb
  sub-directories of 1Mb or more:
    data       2.0Mb
    extdata    2.3Mb
    libs     343.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Running ‘aunitizer.R’ [1s/1s]
  Running ‘runtt.R’ [30s/38s]
Running the tests in ‘tests/runtt.R’ failed.
Last 13 lines of output:
   1. unitizer::unitize(test.file, auto.accept = "new")
   2. unitizer:::unitize_core(...)
   6. unitizer:::unitize_browse(...)
   7. unitizer:::history_capt(history)
  ────────────────────────────────────────────────────────────────────────────────
  
  ⠏ |   0       | testthat.utz1                                                   
  ⠏ |   0       | Unitize                                                         
  ⠋ |   1       | Unitize                                                         
  
  ⠴ |   6       | Unitize                                                         
  ⠏ |  10       | Unitize                                                         
  ⠹ |  23       | Unitize                                                         
  ⠦ |  27       | Unitize                                                         
  ⠇ |  29       | Unitize
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.6Mb
    libs  42.0Mb
Error(s) in re-building vignettes:
--- re-building ‘attribute.plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 46-47 (attribute.plots.Rmd) 
Error: processing vignette 'attribute.plots.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘attribute.plots.Rmd’

--- re-building ‘basic.usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 32-33 (basic.usage.Rmd) 
Error: processing vignette 'basic.usage.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘basic.usage.Rmd’

--- re-building ‘queries.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 40-41 (queries.Rmd) 
Error: processing vignette 'queries.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘queries.Rmd’

--- re-building ‘set.metadata.plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 63-64 (set.metadata.plots.Rmd) 
Error: processing vignette 'set.metadata.plots.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘set.metadata.plots.Rmd’

SUMMARY: processing the following files failed:
  ‘attribute.plots.Rmd’ ‘basic.usage.Rmd’ ‘queries.Rmd’
  ‘set.metadata.plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Data_sources_and_cleaning.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Data_sources_and_cleaning.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: usfertilizer
Loading required package: tidyverse
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.3     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   2.0.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 53-67 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   6.4Mb
Packages required but not available:
  'biomaRt', 'AnnotationHub', 'ensembldb', 'AnnotationFilter',
  'GenomicFeatures', 'GenomicRanges', 'rtracklayer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  21.8Mb
Running examples in ‘V8-Ex.R’ failed
The error most likely occurred in:

> ### Name: wasm
> ### Title: Experimental WebAssembly
> ### Aliases: wasm
> 
> ### ** Examples
> 
> # Load example wasm program
> if(engine_info()$version > 6){
+ instance <- wasm(system.file('wasm/add.wasm', package = 'V8'))
+ instance$exports$add(12, 30)
+ }
Running ‘engine.R’ [0s/0s]
  Comparing ‘engine.Rout’ to ‘engine.Rout.save’ ...4d3
< Using V8 engine 8.7.220.29
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(V8)
  Using V8 engine 8.7.220.29
  > 
  > test_check("V8")
Error(s) in re-building vignettes:
  ...
--- re-building ‘vacuum-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-66 (vacuum-vignette.Rmd) 
Error: processing vignette 'vacuum-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vacuum-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vacuum-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'vaersNDvax', 'vaers', 'vaersND'
Packages required but not available:
  'GenomicAlignments', 'GenomicRanges', 'Rsamtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘valr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 124-136 (valr.Rmd) 
Error: processing vignette 'valr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘valr.Rmd’

SUMMARY: processing the following file failed:
  ‘valr.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 289-294 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 343.3Mb
  sub-directories of 1Mb or more:
    extdata    1.1Mb
    libs     341.6Mb
Error(s) in re-building vignettes:
--- re-building ‘cd.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘cd.Rmd’

--- re-building ‘cfw.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Using libcurl 7.64.1 with LibreSSL/2.8.3
--- finished re-building ‘cfw.Rmd’

--- re-building ‘cytokine.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘cytokine.Rmd’

--- re-building ‘leukemia.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loaded glmnet 4.1-2
Quitting from lines 108-183 (leukemia.Rmd) 
Error: processing vignette 'leukemia.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘leukemia.Rmd’

SUMMARY: processing the following file failed:
  ‘leukemia.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘VarSelLCM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 96-97 (VarSelLCM.Rmd) 
Error: processing vignette 'VarSelLCM.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘VarSelLCM.Rmd’

SUMMARY: processing the following file failed:
  ‘VarSelLCM.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   1.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   4.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/venneuler.Rcheck/00install.out’ for details.
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    help   3.7Mb
Package required but not available: ‘coRdon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘groupsparsewkm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 110-111 (groupsparsewkm.Rmd) 
Error: processing vignette 'groupsparsewkm.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘groupsparsewkm.Rmd’

--- re-building ‘sparsewkm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 92-93 (sparsewkm.Rmd) 
Error: processing vignette 'sparsewkm.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘sparsewkm.Rmd’

SUMMARY: processing the following files failed:
  ‘groupsparsewkm.Rmd’ ‘sparsewkm.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction-to-vimp.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
vimp version 2.2.3: Perform Inference on Algorithm-Agnostic Variable Importance
Loading required package: nnls
Loading required package: gam
Loading required package: splines
Loading required package: foreach
Loaded gam 1.20

Super Learner
Version: 2.0-28
Package created on 2021-05-04

Quitting from lines 410-438 (introduction-to-vimp.Rmd) 
Error: processing vignette 'introduction-to-vimp.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction-to-vimp.Rmd’

--- re-building ‘precomputed-regressions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
vimp version 2.2.3: Perform Inference on Algorithm-Agnostic Variable Importance
Loading required package: nnls
Loading required package: gam
Loading required package: splines
Loading required package: foreach
Loaded gam 1.20

Super Learner
Version: 2.0-28
Package created on 2021-05-04

Loading required namespace: ranger
Quitting from lines 197-225 (precomputed-regressions.Rmd) 
Error: processing vignette 'precomputed-regressions.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘precomputed-regressions.Rmd’

--- re-building ‘types-of-vims.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘types-of-vims.Rmd’

SUMMARY: processing the following files failed:
  ‘introduction-to-vimp.Rmd’ ‘precomputed-regressions.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.3Mb
installed size is 57.1Mb
  sub-directories of 1Mb or more:
    libs  56.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-viridis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 55-59 (intro-to-viridis.Rmd) 
Error: processing vignette 'intro-to-viridis.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro-to-viridis.Rmd’

SUMMARY: processing the following file failed:
  ‘intro-to-viridis.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_virtualPollen.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: viridisLite

Attaching package: 'magrittr'

The following object is masked from 'package:tidyr':

    extract

Quitting from lines 87-105 (using_virtualPollen.Rmd) 
Error: processing vignette 'using_virtualPollen.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘using_virtualPollen.Rmd’

SUMMARY: processing the following file failed:
  ‘using_virtualPollen.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_visdat.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 60-63 (using_visdat.Rmd) 
Error: processing vignette 'using_visdat.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘using_visdat.Rmd’

SUMMARY: processing the following file failed:
  ‘using_visdat.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-vistributions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 44-45 (introduction-to-vistributions.Rmd) 
Error: processing vignette 'introduction-to-vistributions.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction-to-vistributions.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction-to-vistributions.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vivid.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'ranger'

The following object is masked from 'package:randomForest':

    importance


Attaching package: 'ggplot2'

The following object is masked from 'package:randomForest':

    margin

%IncMSE variable importance method used.
Calculating interactions...
Quitting from lines 152-153 (vivid.Rmd) 
Error: processing vignette 'vivid.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘vivid.Rmd’

--- re-building ‘vividQStart.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'ranger'

The following object is masked from 'package:randomForest':

    importance


Attaching package: 'ggplot2'

The following object is masked from 'package:randomForest':

    margin

Calculating interactions...
Quitting from lines 125-126 (vividQStart.Rmd) 
Error: processing vignette 'vividQStart.Rmd' failed with diagnostics:
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--- failed re-building ‘vividQStart.Rmd’

SUMMARY: processing the following files failed:
  ‘vivid.Rmd’ ‘vividQStart.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'cairoDevice', 'gWidgets2RGtk2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 83.1Mb
  sub-directories of 1Mb or more:
    libs  82.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/vortexR.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_voteogram.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 65-68 (intro_to_voteogram.Rmd) 
Error: processing vignette 'intro_to_voteogram.Rmd' failed with diagnostics:
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--- failed re-building ‘intro_to_voteogram.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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Error(s) in re-building vignettes:
  ...
--- re-building ‘benchmarks.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 11-116 (benchmarks.Rmd) 
Error: processing vignette 'benchmarks.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘benchmarks.Rmd’

--- re-building ‘vroom.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘vroom.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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installed size is  8.9Mb
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    doc   5.5Mb
Running examples in ‘water-Ex.R’ failed
The error most likely occurred in:

> ### Name: read.WSdata
> ### Title: Prepares weather station data
> ### Aliases: read.WSdata
> 
> ### ** Examples
> 
> csvfile <- system.file("extdata", "apples.csv", package="water")
> MTLfile <- system.file("extdata", "L7.MTL.txt", package="water")
> WS <- read.WSdata(WSdata = csvfile, date.format = "%d/%m/%Y", 
+                   lat=-35.42222, long= -71.38639, elev=201, height= 2.2,
+                   columns=c("date" = 1, "time" = 2, "radiation" = 3,
+                   "wind" = 4, "RH" = 6, "temp" = 7, "rain" = 8), 
+                   MTL = MTLfile)
Warning in read.WSdata(WSdata = csvfile, date.format = "%d/%m/%Y", lat = -35.42222,  :
  As tz = "", assuming the weather station time zone is Pacific/Auckland
Error in Ops.data.frame(WS.after, WS.prev) : 
  ‘-’ only defined for equally-sized data frames
Calls: read.WSdata -> Ops.data.frame
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 57-80 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
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Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(webex)
  > 
  > test_check("webex")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-compilation.R:16:3): minimal compile ────────────────────────────
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Backtrace:
      █
   1. └─rmarkdown::render(tf, quiet = TRUE) test-compilation.R:16:2
   2.   └─rmarkdown::pandoc_available(required_pandoc, error = TRUE)
   3.     └─rmarkdown:::stop2(paste(msg, collapse = " "))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 31 ]
  Error: Test failures
  Execution halted
installed size is 10.5Mb
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    doc      1.0Mb
Error(s) in re-building vignettes:
--- re-building ‘descStatictics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: webr
Loading required package: moonBook
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Adding missing grouping variables: `sex`
Warning: `cols` is now required when using unnest().
Please use `cols = c(summary)`
Adding missing grouping variables: `sex`
Warning: `cols` is now required when using unnest().
Please use `cols = c(summary)`
Adding missing grouping variables: `sex`, `Dx`
Warning: `cols` is now required when using unnest().
Please use `cols = c(summary)`
Adding missing grouping variables: `sex`, `Dx`
Warning: `cols` is now required when using unnest().
Please use `cols = c(summary)`
Loading required package: rrtable
Welcome to rrtable package
Register inputHandler for chooserInput
Adding missing grouping variables: `sex`
Warning: `cols` is now required when using unnest().
Please use `cols = c(summary)`
Adding missing grouping variables: `sex`
Warning: `cols` is now required when using unnest().
Please use `cols = c(summary)`
--- finished re-building ‘descStatictics.Rmd’

--- re-building ‘plot-htest.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: moonBook
Loading required package: webr
Quitting from lines 37-44 (plot-htest.Rmd) 
Error: processing vignette 'plot-htest.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘plot-htest.Rmd’

SUMMARY: processing the following file failed:
  ‘plot-htest.Rmd’

Error: Vignette re-building failed.
Execution halted
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Error(s) in re-building vignettes:
--- re-building ‘Life_Data_Analysis_Part_I.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 66-83 (Life_Data_Analysis_Part_I.Rmd) 
Error: processing vignette 'Life_Data_Analysis_Part_I.Rmd' failed with diagnostics:
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--- failed re-building ‘Life_Data_Analysis_Part_I.Rmd’

--- re-building ‘Life_Data_Analysis_Part_II.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 188-214 (Life_Data_Analysis_Part_II.Rmd) 
Error: processing vignette 'Life_Data_Analysis_Part_II.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Life_Data_Analysis_Part_II.Rmd’

--- re-building ‘Life_Data_Analysis_Part_III.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 71-86 (Life_Data_Analysis_Part_III.Rmd) 
Error: processing vignette 'Life_Data_Analysis_Part_III.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Life_Data_Analysis_Part_III.Rmd’

SUMMARY: processing the following files failed:
  ‘Life_Data_Analysis_Part_I.Rmd’ ‘Life_Data_Analysis_Part_II.Rmd’
  ‘Life_Data_Analysis_Part_III.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Package required but not available: ‘GO.db’

Packages suggested but not available for checking:
  'org.Hs.eg.db', 'org.Mm.eg.db', 'minet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘wheatmap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 49-74 (wheatmap.Rmd) 
Error: processing vignette 'wheatmap.Rmd' failed with diagnostics:
non-finite location and/or size for viewport
--- failed re-building ‘wheatmap.Rmd’

SUMMARY: processing the following file failed:
  ‘wheatmap.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘counters.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘counters.Rmd’

--- re-building ‘plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-30 (plots.Rmd) 
Error: processing vignette 'plots.Rmd' failed with diagnostics:
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--- failed re-building ‘plots.Rmd’

--- re-building ‘printing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘printing.Rmd’

--- re-building ‘shiny.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘shiny.Rmd’

--- re-building ‘tables.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tables.Rmd’

--- re-building ‘tests_and_coverage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tests_and_coverage.Rmd’

SUMMARY: processing the following file failed:
  ‘plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘intro.Rmd’

--- re-building ‘united_nations.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 81-92 (united_nations.Rmd) 
Error: processing vignette 'united_nations.Rmd' failed with diagnostics:
Can't join on `x$a2` x `y$a2` because of incompatible types.
ℹ `x$a2` is of type <logical>>.
ℹ `y$a2` is of type <character>>.
--- failed re-building ‘united_nations.Rmd’

SUMMARY: processing the following file failed:
  ‘united_nations.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ComplexHeatmap', 'DESeq2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 70-72 (basics.Rmd) 
Error: processing vignette 'basics.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘basics.Rmd’

SUMMARY: processing the following file failed:
  ‘basics.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'RBGL', 'HydeNet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    3. │ └─lattice:::print.trellis(p)
    4. │   └─lattice:::printFunction(x, ...)
    5. │     └─grid::pushViewport(...)
    6. │       └─base::lapply(vps, push.vp, recording)
    7. │         ├─grid:::FUN(X[[i]], ...)
    8. │         └─grid:::push.vp.viewport(X[[i]], ...)
    9. │           └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   10. └─(function (x) ...
   11.   ├─grid::widthDetails(x)
   12.   └─grid:::widthDetails.text(x)
   13.     └─grid:::grid.Call(...)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 276 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignettes.Rmd’ using knitr
Quitting from lines 129-135 (Vignettes.Rmd) 
Error: processing vignette 'Vignettes.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Vignettes.Rmd’

SUMMARY: processing the following file failed:
  ‘Vignettes.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.7Mb
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    libs   9.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘woodsimulatr_basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 251-252 (woodsimulatr_basics.Rmd) 
Error: processing vignette 'woodsimulatr_basics.Rmd' failed with diagnostics:
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--- failed re-building ‘woodsimulatr_basics.Rmd’

SUMMARY: processing the following file failed:
  ‘woodsimulatr_basics.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/wordnet.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   24. │     └─grid::pushViewport(vp, recording = FALSE)
   25. │       └─base::lapply(vps, push.vp, recording)
   26. │         ├─grid:::FUN(X[[i]], ...)
   27. │         └─grid:::push.vp.vpTree(X[[i]], ...)
   28. │           ├─grid:::push.vp(vp$parent, recording)
   29. │           └─grid:::push.vp.viewport(vp$parent, recording)
   30. │             └─grid:::grid.Call.graphics(C_setviewport, vp, TRUE)
   31. └─(function (x) ...
   32.   ├─grid::widthDetails(x)
   33.   └─grid:::widthDetails.text(x)
   34.     └─grid:::grid.Call(...)
  
  [ FAIL 1 | WARN 66 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘evaluating-different-predictor-sets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 89-127 (evaluating-different-predictor-sets.Rmd) 
Error: processing vignette 'evaluating-different-predictor-sets.Rmd' failed with diagnostics:
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--- failed re-building ‘evaluating-different-predictor-sets.Rmd’

SUMMARY: processing the following file failed:
  ‘evaluating-different-predictor-sets.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘intro-to-wpa.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

 Thank you for using the {wpa} R package!
 
 Our analysts have taken every care to ensure that this package runs smoothly and bug-free.
 
 However, if you do happen to encounter any, please report any issues at
 https://github.com/microsoft/wpa/issues/
 
 Happy coding!

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 54-55 (intro-to-wpa.Rmd) 
Error: processing vignette 'intro-to-wpa.Rmd' failed with diagnostics:
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--- failed re-building ‘intro-to-wpa.Rmd’

SUMMARY: processing the following file failed:
  ‘intro-to-wpa.Rmd’

Error: Vignette re-building failed.
Execution halted
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
Error(s) in re-building vignettes:
--- re-building ‘WRI-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
strokeCTdensity              package:WRI               R Documentation

_S_t_r_o_k_e _d_a_t_a: _c_l_i_n_i_c_a_l, _r_a_d_i_o_l_o_g_i_c_a_l _s_c_a_l_a_r _v_a_r_i_a_b_l_e_s _a_n_d _d_e_n_s_i_t_y _c_u_r_v_e_s
_o_f _t_h_e _h_e_m_a_t_o_m_a _o_f _3_9_3 _s_t_r_o_k_e _p_a_t_i_e_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Stroke data: clinical, radiological scalar variables and density
     curves of the hematoma of 393 stroke patients

_F_o_r_m_a_t:

     a list of the following three fields:

     densityCurve: 393-by-101 head CT hematoma densities as
          distributional response

     densitySupport: length 101 common support vector

     predictors: 393-by-9 matrix containing 9 scalar predictors

_R_e_f_e_r_e_n_c_e_s:

     Wasserstein F-tests and confidence bands for the Frechet
     regression of density response curves, Alexander Petersen, Xi Liu
     and Afshin A. Divani, 2019


Quitting from lines 62-73 (WRI-vignette.Rmd) 
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SUMMARY: processing the following file failed:
  ‘WRI-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'qvalue', 'vsn'
Package unavailable to check Rd xrefs: ‘vsn’
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Quitting from lines 63-68 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘vdiffr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘WVPlots_concept.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 21-26 (WVPlots_concept.Rmd) 
Error: processing vignette 'WVPlots_concept.Rmd' failed with diagnostics:
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--- failed re-building ‘WVPlots_concept.Rmd’

--- re-building ‘WVPlots_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 36-37 (WVPlots_examples.Rmd) 
Error: processing vignette 'WVPlots_examples.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘WVPlots_examples.Rmd’

SUMMARY: processing the following files failed:
  ‘WVPlots_concept.Rmd’ ‘WVPlots_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   7.9Mb
Packages required but not available: 'RGtk2', 'cairoDevice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/x13binary.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    bin   4.1Mb
    lib   2.1Mb
Package unavailable to check Rd xrefs: ‘sysfonts’
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 50.6Mb
  sub-directories of 1Mb or more:
    libs  49.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/XLConnect.Rcheck/00install.out’ for details.
Running examples in ‘xlsimple-Ex.R’ failed
The error most likely occurred in:

> ### Name: addXLsheetStd
> ### Title: Add a sheet to the 'Excel' workbook
> ### Aliases: addXLsheetStd
> 
> ### ** Examples
> 
> XL.wb <- getXLsettings()
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/xlsx.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    libs          6.1Mb
Package required but not available: ‘nlmixr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs      2.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘yamlet-introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 307-319 (yamlet-introduction.Rmd) 
Error: processing vignette 'yamlet-introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘yamlet-introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘yamlet-introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gammaproteobacteria.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-27 (gammaproteobacteria.Rmd) 
Error: processing vignette 'gammaproteobacteria.Rmd' failed with diagnostics:
there is no package called 'ggtree'
--- failed re-building ‘gammaproteobacteria.Rmd’

SUMMARY: processing the following file failed:
  ‘gammaproteobacteria.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 50.9Mb
  sub-directories of 1Mb or more:
    libs  50.6Mb
installed size is 48.8Mb
  sub-directories of 1Mb or more:
    libs  48.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ypr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 48-50 (ypr.Rmd) 
Error: processing vignette 'ypr.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ypr.Rmd’

SUMMARY: processing the following file failed:
  ‘ypr.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   4.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘zebu.Rmd’ using knitr
Quitting from lines 291-313 (zebu.Rmd) 
Error: processing vignette 'zebu.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘zebu.Rmd’

SUMMARY: processing the following file failed:
  ‘zebu.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘index.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 350-357 (index.Rmd) 
Error: processing vignette 'index.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘index.Rmd’

SUMMARY: processing the following file failed:
  ‘index.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘aaSEA_Documentation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘aaSEA_Documentation.Rmd’

SUMMARY: processing the following file failed:
  ‘aaSEA_Documentation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 65.9Mb
  sub-directories of 1Mb or more:
    libs  65.6Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm9',
  'BSgenome.Mmusculus.UCSC.mm10'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘WGCNA’

Package suggested but not available for checking: ‘DeconRNASeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Package suggested but not available for checking: ‘HiTC’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ahn.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘ahn.Rmd’

SUMMARY: processing the following file failed:
  ‘ahn.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.8Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    25.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.6Mb
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
installed size is 267.3Mb
  sub-directories of 1Mb or more:
    libs  266.8Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
Packages suggested but not available for checking:
  'pdInfoBuilder', 'AffymetrixDataTestFiles'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.1Mb
Packages suggested but not available for checking:
  'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is 50.4Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    libs  46.2Mb
installed size is 63.2Mb
  sub-directories of 1Mb or more:
    libs  62.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.3Mb
Found the following significant warnings:
  au.c:222:8: warning: 'AudioHardwareGetProperty' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  au.c:229:8: warning: 'AudioDeviceGetProperty' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  au.c:375:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int)') with an expression of type 'au_instance_t *(SEXP, float, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int)') [-Wincompatible-pointer-types]
  au.c:376:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int, int)') with an expression of type 'au_instance_t *(SEXP, float, int, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int, int)') [-Wincompatible-pointer-types]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/audio.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘autocart-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.6-0 (2020-12-14) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: viridis
Loading required package: viridisLite
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-35. For overview type 'help("mgcv-package")'.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
Packages required but not available:
  'fgsea', 'org.Hs.eg.db', 'ConsensusClusterPlus', 'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘aweSOM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 97-101 (aweSOM.Rmd) 
Error: processing vignette 'aweSOM.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘aweSOM.Rmd’

SUMMARY: processing the following file failed:
  ‘aweSOM.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘AzureKeyVault’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   2.9Mb
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    libs  72.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   1.8Mb
Package suggested but not available for checking: ‘ArrayExpress’
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/bapred.Rcheck/00install.out’ for details.
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/baseflow.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'GO.db', 'org.Hs.eg.db', 'reactome.db'
Running examples in ‘batchr-Ex.R’ failed
The error most likely occurred in:

> ### Name: batch_completed
> ### Title: Batch Completed?
> ### Aliases: batch_completed
> 
> ### ** Examples
> 
> path <- tempdir()
> write.csv(mtcars, file.path(path, "file1.csv"))
> batch_config(function(x) TRUE, path, regexp = "[.]csv$")
Error: Directory '/Volumes/Temp/tmp/Rtmp2JD4ue' already contains a '.batchr.rds' file.
Backtrace:
    █
 1. └─batchr::batch_config(function(x) TRUE, path, regexp = "[.]csv$")
 2.   └─chk::err("Directory '", path, "' already contains a '.batchr.rds' file.")
 3.     └─rlang::exec(abort, msg, .subclass = .subclass, !!!args[named])
Execution halted
Running ‘testthat.R’ [7s/61s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  names for target but not for current
  Lengths (1, 0) differ (comparison on first 0 components)
  ── Failure (test-status.R:24:3): batch_file_status all processed successfully ──
  status[c("type", "file", "message")] not identical to structure(...).
  Attributes: < Component "row.names": Numeric: lengths (2, 1) differ >
  Component "type": Lengths (2, 1) differ (string compare on first 1)
  Component "file": Lengths (2, 1) differ (string compare on first 1)
  Component "message": Lengths (2, 1) differ (string compare on first 1)
  ── Failure (test-status.R:28:3): batch_file_status all processed successfully ──
  round(as.numeric(status$time)) not identical to 0.
  Lengths differ: 2 is not 1
  
  [ FAIL 27 | WARN 12 | SKIP 1 | PASS 305 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘batchr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 76-77 (batchr.Rmd) 
Error: processing vignette 'batchr.Rmd' failed with diagnostics:
`x` must be a scalar.
--- failed re-building ‘batchr.Rmd’

SUMMARY: processing the following file failed:
  ‘batchr.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 61.1Mb
  sub-directories of 1Mb or more:
    libs  59.1Mb
installed size is 42.8Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
installed size is 83.2Mb
  sub-directories of 1Mb or more:
    libs  81.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.5Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  13.0Mb
installed size is 69.4Mb
  sub-directories of 1Mb or more:
    libs  68.0Mb
installed size is 83.3Mb
  sub-directories of 1Mb or more:
    libs  82.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   5.3Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  19.5Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  14.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   3.5Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  34.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 143-145 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘example.Rmd’

SUMMARY: processing the following file failed:
  ‘example.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'batchelor', 'kBET', 'splatter', 'lisi', 'harmony', 'dlfUtils'
Packages suggested but not available for checking:
  'beadarrayExampleData', 'lumi'
Running examples in ‘beadarrayFilter-Ex.R’ failed
The error most likely occurred in:

> ### Name: MLM.beadarray
> ### Title: Multi-level Mixed model
> ### Aliases: MLM.beadarray
> ### Keywords: differential expression
> 
> ### ** Examples
> 
> require(beadarrayExampleData)
Loading required package: beadarrayExampleData
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘beadarrayExampleData’
> data(exampleSummaryData)
Warning in data(exampleSummaryData) :
  data set ‘exampleSummaryData’ not found
> exampleSummaryDatalog2 <- channel(exampleSummaryData, "G")[1:40,]
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'object' in selecting a method for function 'channel': object 'exampleSummaryData' not found
Calls: channel -> .handleSimpleError -> h
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 79.0Mb
  sub-directories of 1Mb or more:
    libs  77.5Mb
installed size is 42.6Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
installed size is 60.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  56.8Mb
installed size is 142.8Mb
  sub-directories of 1Mb or more:
    include  142.8Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 244-247 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘analysis.Rmd’

--- re-building ‘methodology.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘methodology.Rmd’

SUMMARY: processing the following file failed:
  ‘analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.9Mb
    libs      2.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      8.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help   1.5Mb
    libs   4.7Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
Package required but not available: ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 74.8Mb
  sub-directories of 1Mb or more:
    libs  74.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Packages required but not available: 'ChemmineR', 'fmcsR', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'GO.db', 'org.Hs.eg.db'
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/BiSEp.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘bit-demo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: bit

Attaching package: 'bit'

The following object is masked from 'package:base':

    xor

Loading required package: ff
Attaching package ff
- getOption("fftempdir")=="/tmp/Rtmp0c3jS4/ff"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: 'ff'

The following objects are masked from 'package:utils':

    write.csv, write.csv2

The following objects are masked from 'package:base':

    is.factor, is.ordered

--- finished re-building ‘bit-demo.Rmd’

--- re-building ‘bit-performance.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: bit

Attaching package: 'bit'

The following object is masked from 'package:base':

    xor

Loading required package: microbenchmark
--- finished re-building ‘bit-performance.Rmd’

--- re-building ‘bit-usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'bit-usage.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘bit-usage.Rmd’

SUMMARY: processing the following file failed:
  ‘bit-usage.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    libs  65.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.8Mb
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  32.8Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is 121.2Mb
  sub-directories of 1Mb or more:
    libs  120.6Mb
installed size is 78.3Mb
  sub-directories of 1Mb or more:
    libs  77.7Mb
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    libs  41.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is 350.5Mb
  sub-directories of 1Mb or more:
    include    8.7Mb
    lib      341.4Mb
installed size is 77.2Mb
  sub-directories of 1Mb or more:
    libs  76.6Mb
installed size is 41.4Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 34.9Mb
  sub-directories of 1Mb or more:
    libs  34.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/Brundle.Rcheck/00install.out’ for details.
installed size is 98.3Mb
  sub-directories of 1Mb or more:
    doc    7.7Mb
    libs  89.9Mb
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  27.3Mb
installed size is 95.6Mb
  sub-directories of 1Mb or more:
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installed size is 14.5Mb
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installed size is 19.7Mb
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Error(s) in re-building vignettes:
--- re-building ‘examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'c3'

The following objects are masked from 'package:graphics':

    grid, legend

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 53-62 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘examples.Rmd’

SUMMARY: processing the following file failed:
  ‘examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 18.7Mb
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    libs  18.6Mb
installed size is  9.6Mb
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installed size is  9.9Mb
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installed size is  7.5Mb
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    libs   6.0Mb
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
converting counts to integer mode
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
>   
> data.mageck = stat.mageck(untreated.list = list(CONTROL1, CONTROL2),
+ treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+ norm.fun="median", extractpattern=expression("^(.+?)(_.+)"),
+ mageckfolder=NULL, sort.criteria="neg", adjust.method="fdr", filename = "TEST" , fdr.pval = 0.05)
sh: mageck: command not found
Warning in system(mageckstring) : error in running command
Warning in file(file, "rt") :
  cannot open file 'TEST.gene_summary.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: stat.mageck -> load.file -> read.table -> file
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘CaRpools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
converting counts to integer mode
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
sh: mageck: command not found
Quitting from lines 1956-1959 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘CaRpools.Rmd’

SUMMARY: processing the following file failed:
  ‘CaRpools.Rmd’

Error: Vignette re-building failed.
Execution halted
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Error(s) in re-building vignettes:
  ...
--- re-building ‘catmaply.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 111-117 (catmaply.Rmd) 
Error: processing vignette 'catmaply.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘catmaply.Rmd’

SUMMARY: processing the following file failed:
  ‘catmaply.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
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Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/CausalGPS.Rcheck/00install.out’ for details.
installed size is  5.2Mb
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installed size is 35.8Mb
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    libs  35.2Mb
installed size is  6.6Mb
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    data      1.6Mb
    extdata   1.1Mb
    libs      3.4Mb
installed size is 132.5Mb
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    libs  132.1Mb
installed size is  7.6Mb
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    libs   6.7Mb
installed size is  6.0Mb
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    data   1.3Mb
    libs   3.2Mb
installed size is  5.3Mb
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    doc    2.4Mb
    libs   1.6Mb
installed size is 13.3Mb
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    data   3.1Mb
    doc    2.1Mb
    libs   7.8Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Packages suggested but not available for checking:
  'GenomicInteractions', 'countreg'
Packages required but not available:
  'ChIPseeker', 'fgsea', 'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.0Mb
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    data   1.8Mb
    libs   4.6Mb
installed size is 14.9Mb
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    libs  14.6Mb
installed size is  7.0Mb
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    data   1.1Mb
    doc    3.5Mb
    libs   1.2Mb
installed size is 10.5Mb
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    libs  10.5Mb
installed size is 20.9Mb
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    libs  20.0Mb
installed size is 35.3Mb
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    libs  33.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/clpAPI.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘clustcurv.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 108-109 (clustcurv.Rmd) 
Error: processing vignette 'clustcurv.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘clustcurv.Rmd’

SUMMARY: processing the following file failed:
  ‘clustcurv.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.8Mb
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installed size is  8.4Mb
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installed size is 11.1Mb
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    libs   9.8Mb
installed size is 35.4Mb
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    libs  35.2Mb
Package required but not available: ‘GenomicInteractions’

Packages suggested but not available for checking:
  'InteractionSet', 'BSgenome.Hsapiens.UCSC.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
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    R      1.4Mb
    libs   3.6Mb
installed size is 15.9Mb
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    libs  13.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘colorspace.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 20-24 (colorspace.Rmd) 
Error: processing vignette 'colorspace.Rmd' failed with diagnostics:
package or namespace load failed for 'ggplot2' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'gtable'
--- failed re-building ‘colorspace.Rmd’

--- re-building ‘hcl-colors.Rnw’ using Sweave
Loading required package: grid
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
--- finished re-building ‘hcl-colors.Rnw’

SUMMARY: processing the following file failed:
  ‘colorspace.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 30.4Mb
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    R      1.5Mb
    libs  28.8Mb
Running ‘testthat.R’ [77s/111s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(conflicted)
  > 
  > test_check("conflicted")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-shim.R:50:3): shimmed library() returns same as unshimmed ─────
  library() not equal to base::library().
  Component "results": Attributes: < Component "dim": Mean relative difference: 5.567929e-05 >
  Component "results": Lengths (53880, 53883) differ (string compare on first 53880)
  Component "results": 29041 string mismatches
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 30 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'conosPanel', 'GO.db', 'org.Hs.eg.db', 'org.Mm.eg.db', 'p2data'
installed size is 11.3Mb
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    libs   9.5Mb
installed size is 58.4Mb
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    libs  57.2Mb
installed size is  9.9Mb
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    R     2.1Mb
    doc   5.6Mb
installed size is  5.3Mb
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    libs          2.6Mb
    sample_data   2.6Mb
installed size is  5.0Mb
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    extdata   3.8Mb
installed size is  8.2Mb
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    doc    1.9Mb
    libs   5.4Mb
installed size is 10.0Mb
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    libs   9.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/cplexAPI.Rcheck/00install.out’ for details.
installed size is  6.4Mb
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    data   1.2Mb
    doc    2.4Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘CPMandPERT.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 104-106 (CPMandPERT.Rmd) 
Error: processing vignette 'CPMandPERT.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘CPMandPERT.Rmd’

--- re-building ‘LESS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-64 (LESS.Rmd) 
Error: processing vignette 'LESS.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘LESS.Rmd’

SUMMARY: processing the following files failed:
  ‘CPMandPERT.Rmd’ ‘LESS.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 28.7Mb
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    libs  27.0Mb
Running ‘testthat.R’ [27s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  SelectPeriodOnDates(...) not equal to `output5`.
  Lengths differ: 92 is not 300
  ── Error (test-SelectPeriod.R:124:3): Decadal ──────────────────────────────────
  Error: Found one or more margin dimensions with the same name and different length in some of the input objects in 'data'.
  Backtrace:
      █
   1. ├─testthat::expect_equal(...) test-SelectPeriod.R:124:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─CSIndicators::SelectPeriodOnData(...)
   5.   └─multiApply::Apply(...)
  
  [ FAIL 2 | WARN 28 | SKIP 0 | PASS 144 ]
  Error: Test failures
  Execution halted
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    R       1.2Mb
    data    1.7Mb
    libs  134.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cubature.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'cubature.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘cubature.Rmd’

--- re-building ‘version2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'version2.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘version2.Rmd’

SUMMARY: processing the following files failed:
  ‘cubature.Rmd’ ‘version2.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
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    libs   4.5Mb
installed size is  8.9Mb
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    R      2.7Mb
    help   1.0Mb
    libs   4.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cycling_data_analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘cycling_data_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘cycling_data_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 23.5Mb
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    libs  22.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘DA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-74 (DA.Rmd) 
Error: processing vignette 'DA.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘DA.Rmd’

SUMMARY: processing the following file failed:
  ‘DA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 58.8Mb
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    libs  57.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘applications.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘applications.Rmd’

--- re-building ‘data.tree.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘data.tree.Rmd’

SUMMARY: processing the following file failed:
  ‘data.tree.Rmd’

Error: Vignette re-building failed.
Execution halted
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installed size is 51.9Mb
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installed size is  9.2Mb
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    libs   8.7Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 76.9Mb
  sub-directories of 1Mb or more:
    libs  74.2Mb
installed size is 37.5Mb
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installed size is  8.7Mb
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    help   1.5Mb
    libs   3.2Mb
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    libs      2.3Mb
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installed size is 20.0Mb
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installed size is  8.8Mb
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    doc    1.1Mb
    libs   6.9Mb
installed size is 57.1Mb
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    libs  56.5Mb
Package required but not available: ‘ALL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘WGCNA’

Package suggested but not available for checking: ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'IHW', 'RNASeqPower', 'zFPKM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘graphviz-mermaid.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 57-79 (graphviz-mermaid.Rmd) 
Error: processing vignette 'graphviz-mermaid.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘graphviz-mermaid.Rmd’

--- re-building ‘node-edge-data-frames.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘node-edge-data-frames.Rmd’

--- re-building ‘selections.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 317-356 (selections.Rmd) 
Error: processing vignette 'selections.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘selections.Rmd’

--- re-building ‘simple-graphs-ndfs-edfs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 165-166 (simple-graphs-ndfs-edfs.Rmd) 
Error: processing vignette 'simple-graphs-ndfs-edfs.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘simple-graphs-ndfs-edfs.Rmd’

--- re-building ‘traversals.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 102-116 (traversals.Rmd) 
Error: processing vignette 'traversals.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘traversals.Rmd’

SUMMARY: processing the following files failed:
  ‘graphviz-mermaid.Rmd’ ‘selections.Rmd’ ‘simple-graphs-ndfs-edfs.Rmd’
  ‘traversals.Rmd’

Error: Vignette re-building failed.
Execution halted
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    libs  10.9Mb
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
Packages required but not available: 'TSCAN', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  7.9Mb
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    help   1.3Mb
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installed size is  8.3Mb
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    libs   7.1Mb
installed size is  7.2Mb
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    libs   2.2Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  10.2Mb
Packages required but not available:
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘userGuide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘userGuide.Rmd’

SUMMARY: processing the following file failed:
  ‘userGuide.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘DSjobtracker.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'magrittr'

The following object is masked from 'package:tidyr':

    extract


Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: viridisLite
Selecting by Total
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 136-155 (DSjobtracker.Rmd) 
Error: processing vignette 'DSjobtracker.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘DSjobtracker.Rmd’

SUMMARY: processing the following file failed:
  ‘DSjobtracker.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Designing-33PC.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 164-165 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Designing-33PC.Rmd’

SUMMARY: processing the following file failed:
  ‘Designing-33PC.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.3Mb
installed size is 155.9Mb
  sub-directories of 1Mb or more:
    libs  155.6Mb
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  23.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Running ‘testthat.R’ [100s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   7.       └─base:::tryCatchList(expr, classes, parentenv, handlers)
   8.         └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.           └─value[[3L]](cond)
  ── Error (test-h5.R:39:3): errors gracefully ───────────────────────────────────
  Error: there is no package called 'hdf5r'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-h5.R:39:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 3 | WARN 6 | SKIP 0 | PASS 545 ]
  Error: Test failures
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs        8.5Mb
    shiny_app   1.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   4.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.4Mb
installed size is 27.5Mb
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    libs  27.3Mb
installed size is 76.5Mb
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    libs  75.7Mb
Error(s) in re-building vignettes:
--- re-building ‘EHRtemporalVariability.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Joining, by = "diagcode1"
# Missing values: 0 cases ( 0%)
# External causes codes: 0 cases ( 0%)
# V codes not mapped: 74330 cases ( 22.82%)
# Total ICD9-CM codes mapped: 146262 cases ( 44.9%)
# Unique ICD9-CM codes mapped: 3020
# Total PheWAS codes: 757
# ICD9 codes not mapped: 105180 cases ( 32.29%)
Quitting from lines 325-330 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘EHRtemporalVariability.Rmd’

SUMMARY: processing the following file failed:
  ‘EHRtemporalVariability.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 85.0Mb
  sub-directories of 1Mb or more:
    libs  84.9Mb
installed size is 47.5Mb
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    libs  46.6Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  15.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.0Mb
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/emstreeR.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘epiflows-class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 104.4Mb
  sub-directories of 1Mb or more:
    libs  102.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    2.1Mb
    libs   2.5Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.2Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
Found the following significant warnings:
  VP_psi.c:843:8: warning: 'gsl_finite' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
  VP_psi.c:843:41: warning: 'gsl_finite' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/ExomeDepth.Rcheck/00install.out’ for details.
Running examples in ‘ExtDist-Ex.R’ failed
The error most likely occurred in:

> ### Name: Beta
> ### Title: The Standard Beta Distribution.
> ### Aliases: Beta dBeta eBeta iBeta lBeta pBeta qBeta rBeta sBeta
> 
> ### ** Examples
> 
> # Parameter estimation for a distribution with known shape parameters
> x <- rBeta(n=500, params=list(shape1=2, shape2=2))
> est.par <- eBeta(x); est.par

Parameters for the Beta distribution. 
(found using the  MOM method.)

 Parameter  Type Estimate
    shape1 shape 2.072842
    shape2 shape 2.014862


> plot(est.par)
Error in loadNamespace(x) : 
  there is no package called ‘PerformanceAnalytics’
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.5Mb
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  16.2Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.7Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.5Mb
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
installed size is 72.3Mb
  sub-directories of 1Mb or more:
    libs  72.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/fedmatch.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Error(s) in re-building vignettes:
--- re-building ‘Data-Model.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dm'

The following object is masked from 'package:stats':

    filter

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 36-39 (Data-Model.Rmd) 
Error: processing vignette 'Data-Model.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Data-Model.Rmd’

--- re-building ‘fishdata-examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

`summarise()` has grouped output by 'site'. You can override using the `.groups` argument.
--- finished re-building ‘fishdata-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘Data-Model.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 40.1Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
installed size is 30.7Mb
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    lib   11.1Mb
    libs  19.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbit_viz.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 157-173 (fitbit_viz.Rmd) 
Error: processing vignette 'fitbit_viz.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘fitbit_viz.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbit_viz.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    4.0Mb
    libs   4.1Mb
installed size is  7.8Mb
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    doc    1.9Mb
    help   2.3Mb
    libs   3.2Mb
installed size is 73.3Mb
  sub-directories of 1Mb or more:
    libs  72.8Mb
installed size is 52.3Mb
  sub-directories of 1Mb or more:
    libs  51.2Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   7.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   5.4Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.1Mb
installed size is 89.6Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.5Mb
    help   1.4Mb
    libs  80.9Mb
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
installed size is 15.4Mb
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    libs  14.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘futureheatwaves.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘futureheatwaves.Rmd’

--- re-building ‘starting_from_netcdf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘starting_from_netcdf.Rmd’

SUMMARY: processing the following file failed:
  ‘futureheatwaves.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 49.1Mb
  sub-directories of 1Mb or more:
    doc   44.4Mb
    libs   4.1Mb
installed size is 11.4Mb
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    data   1.4Mb
    libs   9.4Mb
installed size is 68.3Mb
  sub-directories of 1Mb or more:
    libs  67.8Mb
installed size is 59.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     56.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/gdalcubes.Rcheck/00install.out’ for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.4Mb
    libs      1.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Found the following significant warnings:
  hal.cpp:266:10: warning: 'sem_init' is deprecated [-Wdeprecated-declarations]
  hal.cpp:271:13: warning: 'sem_destroy' is deprecated [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/GENLIB.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.0Mb
installed size is 116.5Mb
  sub-directories of 1Mb or more:
    libs  115.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.1Mb
Package suggested but not available for checking: ‘raster’
Running examples in ‘geosphere-Ex.R’ failed
The error most likely occurred in:

> ### Name: span
> ### Title: Span of polygons
> ### Aliases: span span,SpatialPolygons-method span,matrix-method
> ### Keywords: methods spatial
> 
> ### ** Examples
> 
> pol <- rbind(c(-180,-20), c(-160,5), c(-60, 0), c(-160,-60), c(-180,-20))
> plot(pol)
> lines(pol)
> # lon and lat span in m
> span(pol, fun=max) 
Loading required namespace: raster
Failed with error:  ‘there is no package called ‘raster’’
Error in .local(x, ...) : 
  you need to install the "raster" package to use this function
Calls: span -> span -> .local -> span -> span -> .local
Execution halted
Errors in running code in vignettes:
when running code in ‘geosphere.Rnw’
  ...
           lon       lat
[1,] -57.54653 -28.96994

> span(pol, fun = max)
Loading required namespace: raster
Failed with error:  ‘there is no package called ‘raster’’

  When sourcing ‘geosphere.R’:
Error: you need to install the "raster" package to use this function
Execution halted

  ‘geosphere.Rnw’ using ‘UTF-8’... failed
Error(s) in re-building vignettes:
  ...
--- re-building ‘geosphere.Rnw’ using Sweave
Loading required namespace: raster
Failed with error:  ‘there is no package called ‘raster’’

Error: processing vignette 'geosphere.Rnw' failed with diagnostics:
 chunk 13 
Error in .local(x, ...) : 
  you need to install the "raster" package to use this function

--- failed re-building ‘geosphere.Rnw’

SUMMARY: processing the following file failed:
  ‘geosphere.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘cqn’

Packages suggested but not available for checking:
  'ChAMP', 'clusterProfiler', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  18.8Mb
Error(s) in re-building vignettes:
--- re-building ‘ggPredict.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
`geom_smooth()` using formula 'y ~ x'
Loading required package: ggiraph
Loading required package: ggiraphExtra

Attaching package: 'ggiraphExtra'

The following objects are masked from 'package:moonBook':

    addLabelDf, getMapping

Loading required package: plyr
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘ggPredict.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘gglogo-alphabet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'gglogo'

The following object is masked from 'package:ggplot2':

    fortify

Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Quitting from lines 45-52 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building ‘gglogo-alphabet.Rmd’

SUMMARY: processing the following file failed:
  ‘gglogo-alphabet.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.2Mb
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Matrix
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 185-186 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘fully-customed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘fully-customed.Rmd’

--- re-building ‘using-ggVennDiagram.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 73-81 (using-ggVennDiagram.Rmd) 
Error: processing vignette 'using-ggVennDiagram.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘using-ggVennDiagram.Rmd’

--- re-building ‘using-new-shapes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘using-new-shapes.Rmd’

--- re-building ‘venn-plot-with-more-than-four-sets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘venn-plot-with-more-than-four-sets.Rmd’

SUMMARY: processing the following file failed:
  ‘using-ggVennDiagram.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.3Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 87.4Mb
  sub-directories of 1Mb or more:
    libs  86.1Mb
installed size is 19.5Mb
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    libs  19.2Mb
installed size is 49.2Mb
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    libs  48.5Mb
installed size is 43.7Mb
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    libs  42.8Mb
installed size is 68.1Mb
  sub-directories of 1Mb or more:
    libs           63.6Mb
    test_data       2.0Mb
    vignette_data   1.1Mb
Running ‘AAAtest-all.R’ [52s/52s]
Running the tests in ‘tests/AAAtest-all.R’ failed.
Last 13 lines of output:
  54. zi beta and Gamma (test-zi.R:37:5) - Reason: On CRAN
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Failure (test-basics.R:121:3): Update Binomial ───────────────────────────
  `gm1` not equal to matchForm(gm1, gm1u).
  Component "sdr": Component "gradient.fixed": Mean relative difference: 1.492101e-08
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  In addition: Warning message:
  In checkMatrixPackageVersion() : Package version inconsistency detected.
  TMB was built with Matrix version 1.3.3
  Current Matrix version is 1.3.4
  Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
  Execution halted
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.4Mb
Running examples in ‘gluvarpro-Ex.R’ failed
The error most likely occurred in:

> ### Name: preprocessgvp
> ### Title: preprocessing raw data from continuous glucose monitoring
> ### Aliases: preprocessgvp
> 
> ### ** Examples
> 
> data("datagvp4")
> preprocessgvp(datagvp4)
Error in preprocessgvp(datagvp4) : 
  Variable date and time must have yyyy/mm/dd and hh:mm:ss format.
Execution halted
installed size is 10.0Mb
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installed size is  8.3Mb
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    libs   6.4Mb
installed size is 127.4Mb
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    libs  126.6Mb
installed size is  8.0Mb
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    data   1.4Mb
    libs   6.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gprofiler2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 243-244 (gprofiler2.Rmd) 
Error: processing vignette 'gprofiler2.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘gprofiler2.Rmd’

SUMMARY: processing the following file failed:
  ‘gprofiler2.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.8Mb
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    libs  11.7Mb
installed size is  5.8Mb
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    help   2.4Mb
    libs   3.2Mb
installed size is 11.2Mb
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    libs   9.2Mb
installed size is 18.8Mb
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    libs  16.5Mb
installed size is 31.2Mb
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    libs  30.7Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Package suggested but not available for checking: ‘sf’
Running ‘allier.R’ [1s/1s]
  Comparing ‘allier.Rout’ to ‘allier.Rout.save’ ... OK
  Running ‘blockkr.R’ [1s/1s]
  Comparing ‘blockkr.Rout’ to ‘blockkr.Rout.save’ ... OK
  Running ‘covtable.R’ [1s/1s]
  Comparing ‘covtable.Rout’ to ‘covtable.Rout.save’ ... OK
  Running ‘cv.R’ [1s/2s]
  Comparing ‘cv.Rout’ to ‘cv.Rout.save’ ... OK
  Running ‘cv3d.R’ [1s/2s]
  Comparing ‘cv3d.Rout’ to ‘cv3d.Rout.save’ ... OK
  Running ‘fit.R’ [1s/2s]
  Comparing ‘fit.Rout’ to ‘fit.Rout.save’ ... OK
  Running ‘krige0.R’ [2s/3s]
  Comparing ‘krige0.Rout’ to ‘krige0.Rout.save’ ... OK
  Running ‘line.R’ [1s/2s]
  Comparing ‘line.Rout’ to ‘line.Rout.save’ ... OK
  Running ‘merge.R’ [1s/1s]
  Comparing ‘merge.Rout’ to ‘merge.Rout.save’ ... OK
  Running ‘na.action.R’ [1s/1s]
  Comparing ‘na.action.Rout’ to ‘na.action.Rout.save’ ... OK
  Running ‘rings.R’ [1s/1s]
  Comparing ‘rings.Rout’ to ‘rings.Rout.save’ ... OK
  Running ‘sim.R’ [1s/1s]
  Comparing ‘sim.Rout’ to ‘sim.Rout.save’ ... OK
  Running ‘stars.R’ [1s/2s]
Running the tests in ‘tests/stars.R’ failed.
Last 13 lines of output:
  > v = variogram(log(zinc)~1, meuse)
  > (v.fit = fit.variogram(v, vgm(1, "Sph", 900, 1)))
    model      psill    range
  1   Nug 0.05066243   0.0000
  2   Sph 0.59060780 897.0209
  > k_sp = krige(log(zinc)~1, meuse[-(1:5),], meuse[1:5,], v.fit)
  [using ordinary kriging]
  > k_sp_grd = krige(log(zinc)~1, meuse, meuse.grid, v.fit)
  [using ordinary kriging]
  > 
  > # 1. using sf:
  > suppressPackageStartupMessages(library(sf))
  Error in library(sf) : there is no package called 'sf'
  Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
  Execution halted
installed size is  6.4Mb
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    doc    2.9Mb
    libs   2.8Mb
Running ‘run-tests.R’ [4s/7s]
Running the tests in ‘tests/run-tests.R’ failed.
Last 13 lines of output:
   4: initialize(value, ...)
   5: initialize(value, ...)
   6: methods::new(def, ...)
   7: GSlider$new(toolkit, from, to, by, value, horizontal, handler,     action, container, ...)
   8: .gslider.guiWidgetsToolkitRGtk2(toolkit, from, to, by, value,     horizontal, handler, action, container = container, ...)
   9: .gslider(toolkit, from, to, by, value, horizontal, handler, action,     container = container, ...)
  10: gslider(from = 0, to = 100, by = 1, cont = g)
  11: eval(ei, envir)
  12: eval(ei, envir)
  13: withVisible(eval(ei, envir))
  14: source(i)
  15: FUN(X[[i]], ...)
  16: lapply(X = X, FUN = FUN, ...)
  17: sapply(f, function(i) {    message("testing ", i)    source(i)})
  An irrecoverable exception occurred. R is aborting now ...
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.6Mb
Running ‘testthat.R’ [52s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  > 
  > test_check("gwsem")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On Mac (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-formats.R:115:1): (code run outside of `test_that()`) ─────────
  rmse(bgen$snp_to_F, pgen$snp_to_F) not equal to 0.
  1/1 mismatches
  [1] 1.76 - 0 == 1.76
  
  [ FAIL 1 | WARN 7 | SKIP 1 | PASS 188 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 40-43 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
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    data   1.3Mb
    libs   1.6Mb
installed size is  7.1Mb
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    doc    1.4Mb
    libs   5.1Mb
installed size is 12.4Mb
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    libs  11.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/hdf5r.Rcheck/00install.out’ for details.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  7.4Mb
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    libs   6.7Mb
installed size is 21.2Mb
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    libs  21.1Mb
Error(s) in re-building vignettes:
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 87-94 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘getting-started.Rmd’

--- re-building ‘kmeans-umap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
Using compatibility `.name_repair`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Joining, by = "service_line"
--- finished re-building ‘kmeans-umap.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘heatmaply.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.2.1

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================

Quitting from lines 109-111 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘heatmaply.Rmd’

SUMMARY: processing the following file failed:
  ‘heatmaply.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘hermiter.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'data.table'

The following objects are masked from 'package:dplyr':

    between, first, last

Quitting from lines 542-544 (hermiter.Rmd) 
Error: processing vignette 'hermiter.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘hermiter.Rmd’

SUMMARY: processing the following file failed:
  ‘hermiter.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  19.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hhcartr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 375-379 (hhcartr.Rmd) 
Error: processing vignette 'hhcartr.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘hhcartr.Rmd’

SUMMARY: processing the following file failed:
  ‘hhcartr.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/HierO.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.1Mb
installed size is  8.8Mb
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    highlight   1.0Mb
    libs        7.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.3Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hlidacr)
  > 
  > test_check("hlidacr")
  Error: No root directory found in /Volumes/Builds/packages/high-sierra-x86_64/results/4.1/hlidacr.Rcheck/tests/testthat or its parent directories. Root criterion: contains a file "DESCRIPTION" with contents matching "^Package: "
  Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.0Mb
Package required but not available: ‘bamsignals’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 58.8Mb
  sub-directories of 1Mb or more:
    libs  58.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.6Mb
Package suggested but not available for checking: ‘HTSFilter’
installed size is 38.3Mb
  sub-directories of 1Mb or more:
    libs  38.1Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    doc    1.1Mb
    libs   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hwordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘hwordcloud.Rmd’

SUMMARY: processing the following file failed:
  ‘hwordcloud.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      1.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hyperoverlap-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 51-58 (hyperoverlap-vignette.Rmd) 
Error: processing vignette 'hyperoverlap-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘hyperoverlap-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘hyperoverlap-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.7Mb
Error(s) in re-building vignettes:
--- re-building ‘vignette_iBreakDown_description.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Welcome to DALEX (version: 2.2.0).
Find examples and detailed introduction at: http://ema.drwhy.ai/

randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Warning in randomForest.default(m, y, ...) :
  The response has five or fewer unique values.  Are you sure you want to do regression?
--- finished re-building ‘vignette_iBreakDown_description.Rmd’

--- re-building ‘vignette_iBreakDown_titanic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Welcome to DALEX (version: 2.2.0).
Find examples and detailed introduction at: http://ema.drwhy.ai/

randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Warning in randomForest.default(m, y, ...) :
  The response has five or fewer unique values.  Are you sure you want to do regression?
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 91-92 (vignette_iBreakDown_titanic.Rmd) 
Error: processing vignette 'vignette_iBreakDown_titanic.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘vignette_iBreakDown_titanic.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette_iBreakDown_titanic.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 16.8Mb
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    libs  15.4Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  31.8Mb
Error(s) in re-building vignettes:
--- re-building ‘model_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-32 (model_details.Rmd) 
Error: processing vignette 'model_details.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘model_details.Rmd’

--- re-building ‘parameter_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-31 (parameter_details.Rmd) 
Error: processing vignette 'parameter_details.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘parameter_details.Rmd’

--- re-building ‘resources.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘resources.Rmd’

SUMMARY: processing the following files failed:
  ‘model_details.Rmd’ ‘parameter_details.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  18.3Mb
installed size is  7.4Mb
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    libs   5.4Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.1Mb
    libs         4.5Mb
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     21.8Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs   14.1Mb
    share  10.2Mb
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.6Mb
Package required but not available: ‘RankProd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Running ‘tinytest.R’ [13s/18s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  test_utilities.R..............   10 tests [0;31m1 fails[0m 
  test_utilities.R..............   10 tests [0;31m1 fails[0m 
  test_utilities.R..............   11 tests [0;31m1 fails[0m 
  test_utilities.R..............   11 tests [0;31m1 fails[0m 
  test_utilities.R..............   11 tests [0;31m1 fails[0m 
  test_utilities.R..............   11 tests [0;31m1 fails[0m 
  test_utilities.R..............   11 tests [0;31m1 fails[0m 
  test_utilities.R..............   12 tests [0;31m1 fails[0m 
  test_utilities.R..............   13 tests [0;31m1 fails[0m [0;34m3.1s[0m
  ----- FAILED[xcpt]: test_utilities.R<39--42>
   call| expect_error(moveDLL(quadfn, name = "testname", directory = tempdir(), 
   call| -->    unload = TRUE, overwrite = TRUE), "file can not be copied both 'from' and 'to'")
   diff| No error
  Error: 1 out of 30 tests failed
  Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Error(s) in re-building vignettes:
--- re-building ‘IntGraphTutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: DiagrammeR
Loading required package: DiagrammeRsvg
Loading required package: rsvg
Linking to librsvg 2.48.4
Loading required package: gtools
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 32-34 (IntGraphTutorial.Rmd) 
Error: processing vignette 'IntGraphTutorial.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘IntGraphTutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘IntGraphTutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(intensegRid)
  > 
  > test_check("intensegRid")
  Error: No root directory found in /Volumes/Builds/packages/high-sierra-x86_64/results/4.1/intensegRid.Rcheck/tests/testthat or its parent directories. Root criterion: contains a file "DESCRIPTION" with contents matching "^Package: "
  Execution halted
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘isatabr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'isatabr.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘isatabr.Rmd’

SUMMARY: processing the following file failed:
  ‘isatabr.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          15.6Mb
Package required but not available: ‘lfa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.2Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.7Mb
Errors in running code in vignettes:
when running code in ‘json-opencpu.pdf.asis’
  ...

  When running vignette ‘json-opencpu.pdf.asis’:
Error: No such vignette ‘json-opencpu.pdf.asis’
Execution halted

  ‘json-aaquickstart.Rmd’ using ‘UTF-8’... [1s/1s] OK
  ‘json-apis.Rmd’ using ‘UTF-8’... [0s/1s] OK
  ‘json-paging.Rmd’ using ‘UTF-8’... [0s/1s] OK
  ‘json-mapping.pdf.asis’ using ‘UTF-8’... [1s/1s] OK
  ‘json-opencpu.pdf.asis’ using ‘UTF-8’... failed
Error(s) in re-building vignettes:
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder 'R.rsp' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted
Error in loadVignetteBuilder(pkgdir) : vignette builder 'R.rsp' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted
Error in loadVignetteBuilder(pkgdir) : vignette builder 'R.rsp' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted
SUMMARY: processing the following files failed:
  ‘json-aaquickstart.Rmd’ ‘json-apis.Rmd’ ‘json-paging.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [36s/43s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jtools)
  > 
  > 
  > test_check("jtools")
  
   *** caught segfault ***
  address 0x11127fffc, cause 'memory not mapped'
  Error in find_first_srcref(start) : cannot get ALTVEC DATAPTR during GC
  Calls: test_check ... <Anonymous> -> register_expectation -> %||% -> find_first_srcref
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘general-introduction-to-justifier.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘general-introduction-to-justifier.Rmd’

--- re-building ‘justifier-in-intervention-development.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘justifier-in-intervention-development.Rmd’

--- re-building ‘justifier-in-study-design.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 268-269 (justifier-in-study-design.Rmd) 
Error: processing vignette 'justifier-in-study-design.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘justifier-in-study-design.Rmd’

SUMMARY: processing the following file failed:
  ‘justifier-in-study-design.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/KANT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/kdtools.Rcheck/00install.out’ for details.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  19.2Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/kmcudaR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
* checking examples ...* using check arguments '--no-clean-on-error '
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/LANDD.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs             2.7Mb
    shiny-landsepi   1.3Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  16.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/leidenAlg.Rcheck/00install.out’ for details.
Running examples in ‘LFDREmpiricalBayes-Ex.R’ failed
The error most likely occurred in:

> ### Name: ME.log
> ### Title: Provides Reliable LFDR Estimates by Selecting an Appropriate
> ###   Reference Class
> ### Aliases: ME.log
> ### Keywords: Maximum Entropy Method LFDR Estimation Maximum Likelihood
> ###   Reference Class Separate Reference Class Combined Reference Class
> ###   Maximum Likelihood Estimation
> 
> ### ** Examples
> 
> #import the function ``lfdr.mle'' from package``LFDR.MLE''
> library(LFDR.MLE)
Error in library(LFDR.MLE) : there is no package called ‘LFDR.MLE’
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  10.4Mb
installed size is 66.5Mb
  sub-directories of 1Mb or more:
    libs  65.4Mb
Error(s) in re-building vignettes:
--- re-building ‘augment_lhs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'augment_lhs.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘augment_lhs.Rmd’

--- re-building ‘lhs_basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'lhs_basics.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘lhs_basics.Rmd’

--- re-building ‘lhs_faq.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'lhs_faq.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘lhs_faq.Rmd’

SUMMARY: processing the following files failed:
  ‘augment_lhs.Rmd’ ‘lhs_basics.Rmd’ ‘lhs_faq.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘liayson.Rnw’ using Sweave
Ensembl site unresponsive, trying uswest mirror

Error: processing vignette 'liayson.Rnw' failed with diagnostics:
 chunk 1 
Error in readRDS(bfc[[rid]]) : unknown input format

--- failed re-building ‘liayson.Rnw’

SUMMARY: processing the following file failed:
  ‘liayson.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 35.1Mb
  sub-directories of 1Mb or more:
    libs  34.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    extdata   1.1Mb
    libs      7.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.6Mb
installed size is 42.8Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
Packages required but not available: 'M3C', 'pathifier', 'pathview'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘linkspotterVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘linkspotterVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘linkspotterVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.0Mb
    libs      22.0Mb
    testdata   1.3Mb
installed size is 57.0Mb
  sub-directories of 1Mb or more:
    libs  56.0Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  48.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘lubridate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'lubridate.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘lubridate.Rmd’

SUMMARY: processing the following file failed:
  ‘lubridate.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    help   1.2Mb
    libs   2.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R   4.0Mb
installed size is 87.6Mb
  sub-directories of 1Mb or more:
    libs  87.5Mb
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MADPop-quicktut.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
Packages required but not available: 'TCGAbiolinks', 'maftools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.4Mb
installed size is 133.2Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    libs  125.9Mb
Package required but not available: ‘ssize’

Packages suggested but not available for checking:
  'GEOmetadb', 'WGCNA', 'KEGGgraph', 'pdInfoBuilder', 'lumi',
  'simpleaffy', 'GO.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   4.9Mb
Error(s) in re-building vignettes:
--- re-building ‘latin_square.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 90-91 (latin_square.Rmd) 
Error: processing vignette 'latin_square.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘latin_square.Rmd’

--- re-building ‘make_prior.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 141-145 (make_prior.Rmd) 
Error: processing vignette 'make_prior.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘make_prior.Rmd’

--- re-building ‘neonatal_mortality.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘neonatal_mortality.Rmd’

--- re-building ‘wheat_breeding.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 94-95 (wheat_breeding.Rmd) 
Error: processing vignette 'wheat_breeding.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘wheat_breeding.Rmd’

SUMMARY: processing the following files failed:
  ‘latin_square.Rmd’ ‘make_prior.Rmd’ ‘wheat_breeding.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   1.1Mb
    libs      2.2Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs         11.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.4Mb
    libs   3.4Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      11.3Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Packages required but not available: 'GO.db', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.9Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   9.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  11.6Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  27.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    4.7Mb
    libs   2.2Mb
Error(s) in re-building vignettes:
--- re-building ‘MedLEA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.3     ✔ purrr   0.3.4
✔ tibble  3.1.2     ✔ dplyr   1.0.6
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   1.4.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Loading required package: NLP

Attaching package: 'NLP'

The following object is masked from 'package:ggplot2':

    annotate

Warning in tm_map.SimpleCorpus(., stripWhitespace) :
  transformation drops documents
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 23-39 (MedLEA.Rmd) 
Error: processing vignette 'MedLEA.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘MedLEA.Rmd’

SUMMARY: processing the following file failed:
  ‘MedLEA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  17.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.6Mb
installed size is 89.3Mb
  sub-directories of 1Mb or more:
    libs  88.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/MetaClean.Rcheck/00install.out’ for details.
Package required but not available: ‘GEOmetadb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘metagenomeSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'org.Hs.eg.db', 'annaffy', 'hgu133plus2.db', 'hgu133a.db',
  'hgu95av2.db'
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
installed size is 90.5Mb
  sub-directories of 1Mb or more:
    libs  90.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.7Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    5.4Mb
    libs  19.0Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Error(s) in re-building vignettes:
--- re-building ‘mgcviz.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-35. For overview type 'help("mgcv-package")'.
Loading required package: qgam
Loading required package: ggplot2
Registered S3 method overwritten by 'mgcViz':
  method from  
  +.gg   GGally

Attaching package: 'mgcViz'

The following objects are masked from 'package:stats':

    qqline, qqnorm, qqplot

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 173-181 (mgcviz.rmd) 
Error: processing vignette 'mgcviz.rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘mgcviz.rmd’

SUMMARY: processing the following file failed:
  ‘mgcviz.rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  21.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘mgwrsar-basic_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘mgwrsar-basic_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.4Mb
Packages required but not available: 'dada2', 'DECIPHER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19',
  'BSgenome.Mmusculus.UCSC.mm10'
Running examples in ‘MicroSEC-Ex.R’ failed
The error most likely occurred in:

> ### Name: fun_load_genome
> ### Title: Genome loading function.
> ### Aliases: fun_load_genome
> 
> ### ** Examples
> 
> fun_load_genome("Human")
Error: Install BSgenome.Hsapiens.UCSC.hg38 package.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 118-178 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
Install BSgenome.Hsapiens.UCSC.hg38 package.
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  tprocess.cc:70:9: warning: 'swapcontext' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  tprocess.cc:89:9: warning: 'swapcontext' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  tprocess.cc:148:9: warning: 'getcontext' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  tprocess.cc:157:5: warning: 'makecontext' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  tprocess.cc:159:9: warning: 'swapcontext' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/microsimulation.Rcheck/00install.out’ for details.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    lib    7.0Mb
    libs   3.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 101.3Mb
  sub-directories of 1Mb or more:
    libs  100.7Mb
Package required but not available: ‘GlobalAncova’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   6.3Mb
Packages suggested but not available for checking: 'mixAK', 'BRugs'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   1.6Mb
Package suggested but not available for checking: ‘IlluminaHumanMethylation450kmanifest’
installed size is 339.8Mb
  sub-directories of 1Mb or more:
    libs  339.4Mb
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    libs  34.0Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
Package which this enhances but not available for checking: ‘aMNLFA’
Error(s) in re-building vignettes:
  ...
--- re-building ‘OVA_Predictions_For_MNL.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'OVA_Predictions_For_MNL.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘OVA_Predictions_For_MNL.Rmd’

SUMMARY: processing the following file failed:
  ‘OVA_Predictions_For_MNL.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ms-perks-features.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘ms-perks-features.Rmd’

--- re-building ‘ms-r-python-examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘ms-r-python-examples.Rmd’

--- re-building ‘ms-rmarkdown.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Welcome to DALEX (version: 2.2.1).
Find examples and detailed introduction at: http://ema.drwhy.ai/

`new_observation` argument is NULL. `new_observation_n` observations needed to calculate local explanations are taken from the data.

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 59-75 (ms-rmarkdown.Rmd) 
Error: processing vignette 'ms-rmarkdown.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘ms-rmarkdown.Rmd’

SUMMARY: processing the following file failed:
  ‘ms-rmarkdown.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  101: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  102: test_code(NULL, exprs, env)
  103: source_file(path, child_env(env), wrap = wrap)
  104: FUN(X[[i]], ...)
  105: lapply(test_paths, test_one_file, env = env, wrap = wrap)
  106: force(code)
  107: doWithOneRestart(return(expr), restart)
  108: withOneRestart(expr, restarts[[1L]])
  109: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  110: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, wrap = wrap))
  111: test_files(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap, load_package = load_package)
  112: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap, load_package = load_package, parallel = parallel)
  113: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  114: test_check("modeltime.resample")
  An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘molaR_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: alphahull
Loading required package: rgl
Loading required package: Rvcg
Quitting from lines 58-60 (molaR_vignette.Rmd) 
Error: processing vignette 'molaR_vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘molaR_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘molaR_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.7Mb
    libs   4.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   6.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘international-mortality-tables-overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 235-237 (international-mortality-tables-overview.Rmd) 
Error: processing vignette 'international-mortality-tables-overview.Rmd' failed with diagnostics:
could not find function "whittaker"
--- failed re-building ‘international-mortality-tables-overview.Rmd’

--- re-building ‘using-the-mortalityTables-package.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
--- finished re-building ‘using-the-mortalityTables-package.Rmd’

SUMMARY: processing the following file failed:
  ‘international-mortality-tables-overview.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 65.3Mb
  sub-directories of 1Mb or more:
    libs  64.9Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.4Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   4.0Mb
    libs   3.7Mb
installed size is 45.5Mb
  sub-directories of 1Mb or more:
    libs  45.1Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  17.4Mb
Running examples in ‘mssqlR-Ex.R’ failed
* using check arguments '--no-clean-on-error '
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Packages suggested but not available for checking:
  'switchBox', 'leukemiasEset'
installed size is 80.7Mb
  sub-directories of 1Mb or more:
    libs  80.4Mb
installed size is 104.3Mb
  sub-directories of 1Mb or more:
    doc    5.9Mb
    libs  97.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      █
   1. ├─testthat::expect_null(...) test-unstash.R:2:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─mustashe::stash(...)
   5.   └─mustashe:::check_stash_dir()
   6.     └─base::tryCatch(...)
   7.       └─base:::tryCatchList(expr, classes, parentenv, handlers)
   8.         └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 60 ]
  Error: Test failures
  Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    23.1Mb
    models   1.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Error(s) in re-building vignettes:
--- re-building ‘Installation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Installation.Rmd’

--- re-building ‘neurons-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: rgl
Registered S3 method overwritten by 'nat':
  method             from
  as.mesh3d.ashape3d rgl 
Some nat functions depend on a CMTK installation. See ?cmtk and README.md for details.

Attaching package: 'nat'

The following objects are masked from 'package:base':

    intersect, setdiff, union

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 413-417 (neurons-intro.Rmd) 
Error: processing vignette 'neurons-intro.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘neurons-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘neurons-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘natstrat.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 71-81 (natstrat.Rmd) 
Error: processing vignette 'natstrat.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘natstrat.Rmd’

SUMMARY: processing the following file failed:
  ‘natstrat.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] 329 - 233 ==   96.2
  [2] 197 - 293 ==  -96.2
  [3] 208 - 336 == -128.2
  [4] 318 - 190 ==  128.2
  ── Failure (test-file-functions.R:62:2): grid mappings are read and applied ────
  latlon.data$y not equal to lat.dat[indices].
  4/4 mismatches (average diff: 28)
  [1] 49.5 - 12.4 ==  37.1
  [2] 49.5 - 12.4 ==  37.1
  [3] 40.4 - 59.1 == -18.8
  [4] 40.4 - 59.1 == -18.8
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 45 ]
  Error: Test failures
  Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   5.4Mb
Packages required but not available: 'ndexr', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.6Mb
Package required but not available: ‘KEGGgraph’

Package suggested but not available for checking: ‘NFPdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              5.8Mb
    classic-bugs   1.5Mb
    include        5.7Mb
    libs          17.8Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  25.8Mb
Found the following significant warnings:
  clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
  DIRsubrout.c:505:10: warning: explicitly assigning value of variable of type 'integer' (aka 'int') to itself [-Wself-assign]
  hybrid.c:91:12: warning: 'nlopt_minimize' is deprecated [-Wdeprecated-declarations]
  newuoa.c:184:9: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
  newuoa.c:1241:10: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
  general.c:134:38: warning: 'syscall' is deprecated: first deprecated in macOS 10.12 - syscall(2) is unsupported; please switch to a supported interface. For SYS_kdebug_trace use kdebug_signpost(). [-Wdeprecated-declarations]
  ./f77funcs.h:57:14: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
  ./f77funcs.h:96:6: warning: 'nlopt_get_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
  ./f77funcs.h:104:6: warning: 'nlopt_set_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
  ./f77funcs.h:109:13: warning: 'nlopt_get_stochastic_population' is deprecated [-Wdeprecated-declarations]
  ./f77funcs.h:113:6: warning: 'nlopt_set_stochastic_population' is deprecated [-Wdeprecated-declarations]
  testopt.cpp:218:11: warning: 'nlopt_minimize' is deprecated [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/nloptr.Rcheck/00install.out’ for details.
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs  14.5Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.4Mb
    libs   3.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error(s) in re-building vignettes:
--- re-building ‘discrete.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'discrete.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘discrete.Rmd’

--- re-building ‘functions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'functions.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘functions.Rmd’

--- re-building ‘odin.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'odin.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘odin.Rmd’

SUMMARY: processing the following files failed:
  ‘discrete.Rmd’ ‘functions.Rmd’ ‘odin.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 85.6Mb
  sub-directories of 1Mb or more:
    libs  85.1Mb
Running ‘tinytest.R’ [49s/56s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  testValidate.R................   21 tests [0;32mOK[0m [0;34m0.3s[0m
  ----- FAILED[data]: testApp.R<434--437>
   call| expect_identical_xl(getFavicons("https://reactome.org/content/detail/"), 
   call| -->    "https://reactome.org//templates/favourite/favicon.ico")
   diff| [33m<[39m [33mtarget[39m                                                     
   diff| [34m>[39m [34mcurrent[39m                                                    
   diff| [36m@@ 1 / 1 @@                                                  [39m
   diff| [33m<[39m [90m[1] [39m[33m"https://reactome.org//templates/favourite/favicon.ico"[39m[90m[39m
   diff| [34m>[39m [90m[1] [39m[34m"https://icons.duckduckgo.com/ip3/reactome.org.ico"[39m[90m[39m    
  ----- FAILED[data]: testExport.R<63--66>
   call| expect_true_xl(modtimeReexport > modtimeOriginal, info = "Confirm tarball is overwritten when re-exported")
   diff| Expected TRUE, got FALSE
   info| Confirm tarball is overwritten when re-exported
  Error: 2 out of 572 tests failed
  Execution halted
installed size is 43.4Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
Packages required but not available:
  'org.Hs.eg.db', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'maftools',
  'TCGAbiolinks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.7Mb
Package suggested but not available for checking: ‘paintmap’
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/OpenCL.Rcheck/00install.out’ for details.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs   16.1Mb
    share  10.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   6.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘openland_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'https://zenodo.org/record/3685230/files/SaoLourencoBasin.rda?download=1'
Content type 'application/octet-stream' length 5309066 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

Quitting from lines 264-269 (openland_vignette.Rmd) 
Error: processing vignette 'openland_vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘openland_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘openland_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 196.7Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    libs    186.5Mb
    models    4.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   3.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      4.5Mb
Packages suggested but not available for checking:
  'gurobi', 'ggtree', 'lpsymphony'
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   5.7Mb
Error(s) in re-building vignettes:
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Rcpp_API.Rmd’

--- re-building ‘customisation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘customisation.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘graph_packing.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘intro.Rmd’

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 204-226 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘progressive_packing.Rmd’

SUMMARY: processing the following file failed:
  ‘progressive_packing.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘genbankr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GO.db', 'org.Dr.eg.db', 'org.Hs.eg.db', 'org.Mm.eg.db', 'p2data',
  'scde'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   5.2Mb
Package suggested but not available for checking: ‘DECIPHER’
installed size is 56.8Mb
  sub-directories of 1Mb or more:
    doc    9.3Mb
    libs  47.0Mb
Error(s) in re-building vignettes:
--- re-building ‘PandemicLP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 28-30 (PandemicLP.Rmd) 
Error: processing vignette 'PandemicLP.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘PandemicLP.Rmd’

--- re-building ‘PandemicLP_SumRegions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'http://github.com/CovidLP/PandemicLP/raw/master/temp/PandemicLP_SumRegions.rda'
Content type 'application/octet-stream' length 13851069 bytes (13.2 MB)
==================================================
downloaded 13.2 MB

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Quitting from lines 172-175 (PandemicLP_SumRegions.Rmd) 
Error: processing vignette 'PandemicLP_SumRegions.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘PandemicLP_SumRegions.Rmd’

SUMMARY: processing the following files failed:
  ‘PandemicLP.Rmd’ ‘PandemicLP_SumRegions.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Logging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'Logging.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘Logging.Rmd’

--- re-building ‘Parallel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'Parallel.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘Parallel.Rmd’

SUMMARY: processing the following files failed:
  ‘Logging.Rmd’ ‘Parallel.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.9Mb
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installed size is 18.5Mb
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installed size is  6.2Mb
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    doc    1.2Mb
    libs   3.8Mb
Packages required but not available: 'maftools', 'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'jetset', 'Mfuzz', 'WGCNA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/pbdPROF.Rcheck/00install.out’ for details.
installed size is  6.7Mb
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    examples   1.7Mb
installed size is  5.6Mb
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    libs      2.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/pcaL1.Rcheck/00install.out’ for details.
installed size is 12.2Mb
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installed size is 104.5Mb
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installed size is 35.5Mb
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installed size is  7.2Mb
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Error(s) in re-building vignettes:
--- re-building ‘pdxTrees-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 93-133 (pdxTrees-vignette.Rmd) 
Error: processing vignette 'pdxTrees-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘pdxTrees-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘pdxTrees-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
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Package suggested but not available for checking: ‘ptmixed’
Running examples in ‘pencal-Ex.R’ failed
The error most likely occurred in:

> ### Name: simulate_prclmm_data
> ### Title: Simulate data that can be used to fit the PRC-LMM model
> ### Aliases: simulate_prclmm_data
> 
> ### ** Examples
> 
> # generate example data
> simdata = simulate_prclmm_data(n = 20, p = 10, 
+                         p.relev = 4, seed = 1)
> # view the longitudinal markers:
> library(ptmixed)
Error in library(ptmixed) : there is no package called ‘ptmixed’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pencal-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 135-144 (pencal-vignette.Rmd) 
Error: processing vignette 'pencal-vignette.Rmd' failed with diagnostics:
there is no package called 'ptmixed'
--- failed re-building ‘pencal-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘pencal-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  43.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/permGPU.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
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    help   1.2Mb
    libs   3.7Mb
installed size is  7.9Mb
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    doc    1.5Mb
    libs   3.9Mb
installed size is  5.7Mb
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    doc       1.5Mb
    extdata   3.1Mb
installed size is 32.9Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘Advanced_Usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Advanced_Usage.Rmd’

--- re-building ‘Basic_Use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 30-32 (Basic_Use.Rmd) 
Error: processing vignette 'Basic_Use.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Basic_Use.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced_Usage.Rmd’ ‘Basic_Use.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 12.1Mb
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installed size is 25.5Mb
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installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   8.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.8Mb
Package required but not available: ‘enviGCMS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘polynomials.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'polynomials.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘polynomials.Rmd’

SUMMARY: processing the following file failed:
  ‘polynomials.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
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    doc    1.7Mb
    libs   1.5Mb
installed size is  8.7Mb
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    extdata   4.7Mb
    libs      2.7Mb
installed size is 48.9Mb
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installed size is 13.9Mb
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installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQnote.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘PPQnote.Rmd’

--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 130-131 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘PPQplan-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘PPQplan-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘predict3d.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: predict3d
Loading required package: rgl
Quitting from lines 55-58 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘predict3d.Rmd’

SUMMARY: processing the following file failed:
  ‘predict3d.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI', 'lpsymphony'
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   9.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in getPrisma(studyStatus) :
  prismaFormat is null so attempting to make automatic one from studyStatus
Warning in getFormatNode(prismaFormat) :
  fontSize param not passed in prismaFormat
Quitting from lines 43-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘PRISMA.Rmd’

SUMMARY: processing the following file failed:
  ‘PRISMA.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 39-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘PRISMA.Rmd’

--- re-building ‘exclusionflowcharts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-31 (exclusionflowcharts.Rmd) 
Error: processing vignette 'exclusionflowcharts.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘exclusionflowcharts.Rmd’

SUMMARY: processing the following files failed:
  ‘PRISMA.Rmd’ ‘exclusionflowcharts.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.5Mb
installed size is 14.1Mb
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    extdata   7.4Mb
    libs      5.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      2.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/proj4.Rcheck/00install.out’ for details.
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  35.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   3.0Mb
installed size is 24.0Mb
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installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
Errors in running code in vignettes:
when running code in ‘CBS.tex.rsp’
  ...

> t0 <- Sys.time()

> R.utils::use("R.utils")

> R.rsp <- R.oo::Package("R.rsp")

  When sourcing ‘CBS.R’:
Error: Package is not installed: R.rsp
Execution halted

  ‘CBS.tex.rsp’... failed
  ‘PairedPSCBS.tex.rsp’... [25s/31s] OK
Running examples in ‘pscl-Ex.R’ failed
The error most likely occurred in:

> ### Name: hurdletest
> ### Title: Testing for the Presence of a Zero Hurdle
> ### Aliases: hurdletest
> ### Keywords: regression
> 
> ### ** Examples
> 
> data("bioChemists", package = "pscl")
> fm <- hurdle(art ~ ., data = bioChemists, dist = "negbin", zero = "negbin")
> hurdletest(fm)
Loading required namespace: car
Failed with error:  ‘there is no package called ‘stringi’’
Error in hurdletest(fm) : requireNamespace("car") is not TRUE
Calls: hurdletest -> stopifnot
Execution halted
Errors in running code in vignettes:
when running code in ‘countreg.Rnw’
  ...

> library("MASS")

> library("car")
Loading required package: carData

  When sourcing ‘countreg.R’:
Error: package or namespace load failed for ‘car’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘stringi’
Execution halted

  ‘countreg.Rnw’... failed
Error(s) in re-building vignettes:
  ...
--- re-building ‘countreg.Rnw’ using Sweave
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Loading required package: carData

Error: processing vignette 'countreg.Rnw' failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error : package or namespace load failed for ‘car’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘stringi’

--- failed re-building ‘countreg.Rnw’

SUMMARY: processing the following file failed:
  ‘countreg.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
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    doc    1.8Mb
    libs   3.0Mb
installed size is  8.3Mb
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installed size is 11.0Mb
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    libs  10.5Mb
installed size is 48.4Mb
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installed size is 23.5Mb
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    libs  22.5Mb
installed size is 47.1Mb
  sub-directories of 1Mb or more:
    libs  46.7Mb
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Running examples in ‘pulseTD-Ex.R’ failed
The error most likely occurred in:

> ### Name: estimateExpression
> ### Title: Estimated Expression
> ### Aliases: estimateExpression
> 
> ### ** Examples
> 
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Error in library(TxDb.Hsapiens.UCSC.hg19.knownGene) : 
  there is no package called ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 63-65 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘other-langs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'other-langs.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘other-langs.Rmd’

SUMMARY: processing the following file failed:
  ‘other-langs.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Data_Model.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Data_Model.Rmd’

--- re-building ‘Example_Save_Data_as_CSV.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Example_Save_Data_as_CSV.Rmd’

--- re-building ‘Maps_and_Timeseries_Plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in monitor_dailyStatistic(PacNW, FUN = mean, minHours = 20) :
  Found 2 timezones. Only 'America/Los_Angeles' will be used
--- finished re-building ‘Maps_and_Timeseries_Plots.Rmd’

--- re-building ‘NowCast.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘NowCast.Rmd’

--- re-building ‘PWFSLSmoke.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 161-162 (PWFSLSmoke.Rmd) 
Error: processing vignette 'PWFSLSmoke.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘PWFSLSmoke.Rmd’

SUMMARY: processing the following file failed:
  ‘PWFSLSmoke.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    libs         2.7Mb
    staticdocs   3.3Mb
installed size is 85.5Mb
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installed size is 70.2Mb
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    libs  69.9Mb
installed size is 15.3Mb
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    libs  15.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  10.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs     32.9Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       3.0Mb
    libs      1.3Mb
installed size is  7.9Mb
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installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 10.8Mb
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    data   3.8Mb
    libs   6.6Mb
installed size is  9.2Mb
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    data   4.5Mb
    libs   4.0Mb
installed size is  9.8Mb
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    data   2.1Mb
    doc    5.8Mb
    libs   1.3Mb
Error(s) in re-building vignettes:
--- re-building ‘a01_GettingStarted.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 40-78 (a01_GettingStarted.Rmd) 
Error: processing vignette 'a01_GettingStarted.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘a01_GettingStarted.Rmd’

--- re-building ‘a02_VitalRates.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘a02_VitalRates.Rmd’

--- re-building ‘a03_LifeHistoryTraits.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘a03_LifeHistoryTraits.Rmd’

--- re-building ‘a04_AgeFromStage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘a04_AgeFromStage.Rmd’

SUMMARY: processing the following file failed:
  ‘a01_GettingStarted.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘KEGGgraph’
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets        9.7Mb
    super-tiny-icons   1.0Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   7.0Mb
Package required but not available: ‘InterpretMSSpectrum’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   4.5Mb
Running examples in ‘rapbase-Ex.R’ failed
The error most likely occurred in:

> ### Name: getRapPackages
> ### Title: Get all installed Rapporteket packages
> ### Aliases: getRapPackages
> 
> ### ** Examples
> 
> getRapPackages()
Warning in utils::packageDescription(pkg) :
  DESCRIPTION file of package 'psychonetrics' is missing or broken
Error: $ operator is invalid for atomic vectors
Execution halted
Running ‘testthat.R’ [48s/70s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       █
    1. ├─testthat::expect_true(is.vector(getRapPackages())) test-miscellaneous-functions.R:4:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::is.vector(getRapPackages())
    5. └─rapbase::getRapPackages()
    6.   └─base::sapply(allPkg$Package, isPkgRapReg)
    7.     └─base::lapply(X = X, FUN = FUN, ...)
    8.       └─rapbase:::FUN(X[[i]], ...)
    9.         └─base::grepl(...)
   10.           └─base::is.factor(x)
  
  [ FAIL 1 | WARN 4 | SKIP 3 | PASS 85 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rappdirs)
  > 
  > # ensure CRAN settings don't affect tests
  > Sys.unsetenv("R_USER_DATA_DIR")
  > Sys.unsetenv("R_USER_CONFIG_DIR")
  > Sys.unsetenv("R_USER_CACHE_DIR")
  > 
  > test_check("rappdirs")
  Error in loadNamespace(x) : there is no package called 'withr'
  Calls: test_check ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   9.7Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    libs   6.9Mb
Package unavailable to check Rd xrefs: ‘rgdal’
installed size is 60.8Mb
  sub-directories of 1Mb or more:
    libs  60.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   7.6Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   3.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/rbedrock.Rcheck/00install.out’ for details.
installed size is 41.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  38.3Mb
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/Rblpapi.Rcheck/00install.out’ for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   4.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.3Mb
    po    2.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/Rcplex.Rcheck/00install.out’ for details.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   6.2Mb
    libs      2.2Mb
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RcppClassic.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.2Mb
installed size is 32.9Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RcppMeCab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RcppMLPACK.Rcheck/00install.out’ for details.
installed size is 41.4Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      28.1Mb
    libs     11.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      4.8Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    include        1.7Mb
    jsonexamples   3.8Mb
    libs          12.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/rcrypt.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rdf_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 41-42 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘rdf_intro.Rmd’

SUMMARY: processing the following file failed:
  ‘rdf_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RDieHarder.Rcheck/00install.out’ for details.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ReDaMoR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 157-163 (ReDaMoR.Rmd) 
Error: processing vignette 'ReDaMoR.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘ReDaMoR.Rmd’

SUMMARY: processing the following file failed:
  ‘ReDaMoR.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   3.1Mb
Package required but not available: ‘maftools’

Package suggested but not available for checking: ‘TCGAbiolinks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    libs      3.2Mb
    swagger   1.4Mb
Running ‘testthat.R’ [7s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Class:   simpleError/error/condition
  Backtrace:
      █
   1. ├─testthat::expect_error(runAllChunks("test-rmarkdown.Rmd"), NA) test-rmarkdown.R:14:4
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat:::.capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─retrosheet:::runAllChunks("test-rmarkdown.Rmd")
   7.   └─rmarkdown::render(rmd, output_file = tempR, quiet = TRUE) test-rmarkdown.R:10:8
   8.     └─rmarkdown::pandoc_available(required_pandoc, error = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 59 ]
  Error: Test failures
  Execution halted
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
Running ‘ChecksumFile.R’ [2s/3s]
  Running ‘GenericDataFile.R’ [2s/4s]
Running the tests in ‘tests/GenericDataFile.R’ failed.
Last 13 lines of output:
  +   stopifnot(!isFile(dfLC))
  +   stopifnot(isFile(dfL))
  +   stopifnot(isFile(df))
  + 
  +   # Cleanup
  +   file.remove(getPathname(dfL))
  + } # if (.Platform$OS.type == "windows")
  GenericDataFile:
  Name: 1.2(a)
  Tags: 
  Full name: 1.2(a)
  Pathname: /Volumes/Temp/tmp/RtmpIGOwCA/1.2(a).txt
  File size: 153 B (153 bytes)
  Error: getChecksum(dfLC) == getChecksum(df) is not TRUE
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘rfm-customer-level-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following object is masked from 'package:kableExtra':

    group_rows

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 231-254 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘rfm-customer-level-data.Rmd’

--- re-building ‘rfm-transaction-level-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following object is masked from 'package:kableExtra':

    group_rows

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 227-251 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘rfm-transaction-level-data.Rmd’

SUMMARY: processing the following files failed:
  ‘rfm-customer-level-data.Rmd’ ‘rfm-transaction-level-data.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 273.2Mb
  sub-directories of 1Mb or more:
    doc         3.4Mb
    libs      265.9Mb
    pictures    1.3Mb
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      1.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rgeoprofile.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 141-142 (rgeoprofile.Rmd) 
Error: processing vignette 'rgeoprofile.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘rgeoprofile.Rmd’

SUMMARY: processing the following file failed:
  ‘rgeoprofile.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc     1.7Mb
    fonts   1.5Mb
    libs    7.3Mb
Error(s) in re-building vignettes:
  ...
sh: line 1: 77473 Abort trap: 6           '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/Rtmpi6MGHe/file12e8b4150b60c' 2>&1 < '/Volumes/Temp/tmp/Rtmpi6MGHe/file12e8b19dfef54'
--- re-building ‘WebGL.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- re-building ‘pkgdown.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘pkgdown.Rmd’

sh: line 1: 77533 Abort trap: 6           '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/Rtmpi6MGHe/file12e8b64a9989e' 2>&1 < '/Volumes/Temp/tmp/Rtmpi6MGHe/file12e8b3a62e0b3'
--- re-building ‘rgl.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- re-building ‘transparency.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘transparency.Rmd’

SUMMARY: processing the following files failed:
  ‘WebGL.Rmd’ ‘rgl.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.9Mb
    libs  17.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/Rhpc.Rcheck/00install.out’ for details.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RInside.Rcheck/00install.out’ for details.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.4Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Running examples in ‘RiverLoad-Ex.R’ failed
The error most likely occurred in:

> ### Name: method4
> ### Title: Load estimation with time-weighted concentration method
> ### Aliases: method4
> ### Keywords: univ
> 
> ### ** Examples
> 
> data("flow.data1", "conc.data1")
> union<-db.union(flow.data1, conc.data1)
> met4<-method4(union, 2)
> met4.month<-method4(union, 2, "month")
Error in x[[jj]][iseq] <- vjj : replacement has length zero
Calls: method4 -> [<- -> [<-.data.frame
Execution halted
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

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 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Package suggested but not available for checking: ‘golubEsets’
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
Package unavailable to check Rd xrefs: ‘glue’
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 54.2Mb
  sub-directories of 1Mb or more:
    libs  53.5Mb
Package required but not available: ‘hdf5r’

Packages suggested but not available for checking:
  'org.Hs.eg.db', 'reactome.db', 'fgsea'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    rmd   8.2Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RMark.Rcheck/00install.out’ for details.
installed size is 68.5Mb
  sub-directories of 1Mb or more:
    libs  67.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RmecabKo.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs       1.1Mb
    minizinc   3.2Mb
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    libs  39.6Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/Rmpi.Rcheck/00install.out’ for details.
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    libs  51.3Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  19.2Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  19.0Mb
installed size is 96.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     94.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Error(s) in re-building vignettes:
--- re-building ‘robin.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: gprege
Loading required package: gptk
Loading required package: Matrix
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.6-0 (2020-12-14) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following object is masked from 'package:Matrix':

    det

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: viridis
Loading required package: viridisLite
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
Loading required package: qpdf
Quitting from lines 97-98 (robin.Rmd) 
Error: processing vignette 'robin.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘robin.Rmd’

SUMMARY: processing the following file failed:
  ‘robin.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RobLoxBioC.Rcheck/00install.out’ for details.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  29.7Mb
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.9Mb
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.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/ROracle.Rcheck/00install.out’ for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   2.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/rpanel.Rcheck/00install.out’ for details.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rpolyhedra.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 49-88 (Rpolyhedra.Rmd) 
Error: processing vignette 'Rpolyhedra.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Rpolyhedra.Rmd’

SUMMARY: processing the following file failed:
  ‘Rpolyhedra.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/Rpoppler.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RPostgreSQL.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rpredictit-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 54-56 (rpredictit-vignette.Rmd) 
Error: processing vignette 'rpredictit-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘rpredictit-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘rpredictit-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
installed size is 89.3Mb
  sub-directories of 1Mb or more:
    libs  88.7Mb
Running ‘RQuantlib.R’ [1s/1s]
Running the tests in ‘tests/RQuantlib.R’ failed.
Last 13 lines of output:
  +                             settleDate=as.Date('2002-2-15'),
  +                             dt=0.25,
  +                             interpWhat='discount', interpHow='loglinear')
  > discountCurve <- DiscountCurve(discountCurve.param, list(flat=0.05))
  > 
  > ZeroCouponBond(bond, discountCurve, dateparams)
  
   *** caught segfault ***
  address 0x0, cause 'memory not mapped'
  
  Traceback:
   1: ZeroBondWithRebuiltCurve(bond, c(discountCurve$table$date), discountCurve$table$zeroRates,     dateparams)
   2: ZeroCouponBond.default(bond, discountCurve, dateparams)
   3: ZeroCouponBond(bond, discountCurve, dateparams)
  An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/rrd.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RSclient.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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 26.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  24.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is 46.3Mb
  sub-directories of 1Mb or more:
    libs  45.7Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is 176.0Mb
  sub-directories of 1Mb or more:
    R       1.6Mb
    doc     4.5Mb
    libs  169.3Mb
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  34.0Mb
installed size is 256.2Mb
  sub-directories of 1Mb or more:
    lib    28.7Mb
    libs  224.8Mb
installed size is 89.3Mb
  sub-directories of 1Mb or more:
    libs  88.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is 94.0Mb
  sub-directories of 1Mb or more:
    libs  93.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.1Mb
    projects   2.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 29.5Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  20.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.5Mb
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  45.3Mb
Packages required but not available:
  'GSVAdata', 'clusterProfiler', 'org.Hs.eg.db', 'rWikiPathways'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 41.0Mb
  sub-directories of 1Mb or more:
    libs  40.3Mb
installed size is 62.9Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     58.5Mb
Found the following significant warnings:
  parser.cc:302:11: warning: 'daemon' is deprecated: first deprecated in macOS 10.5 - Use posix_spawn APIs instead. [-Wdeprecated-declarations]
Found the following additional notes/warnings:
  Non-staged installation was used
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RVowpalWabbit.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
    test   4.5Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs    8.1Mb
    yacas   1.3Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs    8.8Mb
    yacas   1.3Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs     30.8Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   9.9Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is 39.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs  37.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.7Mb
Packages suggested but not available for checking: 'GO.db', 'org.Sc.sgd.db'
Errors in running code in vignettes:
when running code in ‘sandwich-OOP.Rnw’
  ...

> library("AER")
Loading required package: car
Loading required package: carData
Error: package or namespace load failed for ‘car’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘stringi’

  When sourcing ‘sandwich-OOP.R’:
Error: package ‘car’ could not be loaded
Execution halted

  ‘sandwich-CL.Rnw’... [9s/13s] OK
  ‘sandwich-OOP.Rnw’... failed
  ‘sandwich.Rnw’... [1s/1s] OK
Error(s) in re-building vignettes:
--- re-building ‘sandwich-CL.Rnw’ using Sweave
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric


Attaching package: ‘pcse’

The following object is masked from ‘package:sandwich’:

    vcovPC

Classes and Methods for R developed in the
Political Science Computational Laboratory
Department of Political Science
Stanford University
Simon Jackman
hurdle and zeroinfl functions by Achim Zeileis
--- finished re-building ‘sandwich-CL.Rnw’

--- re-building ‘sandwich-OOP.Rnw’ using Sweave
Loading required package: car
Loading required package: carData
Error: package or namespace load failed for ‘car’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘stringi’

Error: processing vignette 'sandwich-OOP.Rnw' failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error : package ‘car’ could not be loaded

--- failed re-building ‘sandwich-OOP.Rnw’

--- re-building ‘sandwich.Rnw’ using Sweave

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

--- finished re-building ‘sandwich.Rnw’

SUMMARY: processing the following file failed:
  ‘sandwich-OOP.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    bin   4.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   3.1Mb
Package required but not available: ‘ADAPTS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/SC.MEB.Rcheck/00install.out’ for details.
Packages required but not available: 'ALL', 'ConsensusClusterPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.0Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  14.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   2.5Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs    16.7Mb
    models   1.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Package required but not available: ‘widgetTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   9.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: ‘muscle’
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.2Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
Packages suggested but not available for checking:
  'hdf5r', 'MAST', 'monocle'
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   7.8Mb
Running ‘testthat.R’ [28s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("Seurat")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (19)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_load_10X.R:34:1): (code run outside of `test_that()`) ───────────
  Error: Please install hdf5r to read HDF5 files
  Backtrace:
      █
   1. └─Seurat::Load10X_Spatial(data.dir = "../testdata/visium") test_load_10X.R:34:0
   2.   └─Seurat::Read10X_h5(...)
  
  [ FAIL 1 | WARN 9 | SKIP 19 | PASS 587 ]
  Error: Test failures
  Execution halted
installed size is 285.4Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    libs    278.6Mb
    sqlite    1.5Mb
Package unavailable to check Rd xrefs: ‘tripack’
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    www   8.8Mb
Package required but not available: ‘maftools’

Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg19', 'copynumber'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.9Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  11.6Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
Package required but not available: ‘qpgraph’

Package suggested but not available for checking: ‘clipper’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘simplevis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning: Removed 2 rows containing non-finite values (stat_density).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
`summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
`summarise()` has grouped output by 'sex'. You can override using the `.groups` argument.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 290-292 (simplevis.Rmd) 
Error: processing vignette 'simplevis.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘simplevis.Rmd’

SUMMARY: processing the following file failed:
  ‘simplevis.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.3Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  20.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   6.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.0Mb
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
Package required but not available: ‘maftools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.7Mb
    libs   9.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 136-139 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
package rpanel is required
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    2.2Mb
    libs   6.7Mb
Error(s) in re-building vignettes:
--- re-building ‘built_in.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘built_in.Rmd’

--- re-building ‘cloning.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘cloning.Rmd’

--- re-building ‘novel_solutions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘novel_solutions.Rmd’

--- re-building ‘understanding_sortable_js.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 85-86 (understanding_sortable_js.Rmd) 
Error: processing vignette 'understanding_sortable_js.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘understanding_sortable_js.Rmd’

--- re-building ‘using_custom_css.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘using_custom_css.Rmd’

SUMMARY: processing the following file failed:
  ‘understanding_sortable_js.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'r2cytoscape', 'hgu95av2.db', 'ALL', 'org.Hs.eg.db'
Package unavailable to check Rd xrefs: ‘ALL’
Error(s) in re-building vignettes:
--- re-building ‘SourceSet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Identifing all possible orderings..
Total run time: 1.23 secs
Identifing all possible orderings..
Total run time: 0.61 secs
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.2Mb
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs  34.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  10.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    help   3.1Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   6.1Mb
    etc   1.3Mb
Found the following significant warnings:
  Warning: namespace ‘xcms’ is not available and has been replaced
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/specmine.datasets.Rcheck/00install.out’ for details.
Failed with error:  'package 'MSnbase' could not be loaded'
  Error loading dataset 'spinalCord':
   Error in .requirePackage(package) : 
    unable to find required package 'xcms'
  
  The dataset(s) may use package(s) not declared in the DESCRIPTION file.
Packages suggested but not available for checking:
  'MAIT', 'KEGGgraph', 'rcytoscapejs'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.4Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      3.6Mb
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  49.3Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
installed size is 69.3Mb
  sub-directories of 1Mb or more:
    libs  68.9Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    include  10.2Mb
    lib       1.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘differences-gw-cow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘differences-gw-cow.Rmd’

--- re-building ‘statelists.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 28-30 (statelists.Rmd) 
Error: processing vignette 'statelists.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘statelists.Rmd’

SUMMARY: processing the following file failed:
  ‘statelists.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Getting_Started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 206-208 (Getting_Started.Rmd) 
Error: processing vignette 'Getting_Started.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Getting_Started.Rmd’

SUMMARY: processing the following file failed:
  ‘Getting_Started.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.7Mb
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  10.0Mb
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    libs  35.2Mb
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   12.   │ └─base::asNamespace(ns)
   13.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   14.     ├─base::namespaceImportFrom(...)
   15.     │ └─base::asNamespace(ns)
   16.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   17.       ├─base::namespaceImportFrom(...)
   18.       │ └─base::asNamespace(ns)
   19.       └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   20.         └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   21.           └─base:::withOneRestart(expr, restarts[[1L]])
   22.             └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 216 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘shinygains.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘shinygains.Rmd’

--- re-building ‘suddengains-tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 472-479 (suddengains-tutorial.Rmd) 
Error: processing vignette 'suddengains-tutorial.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘suddengains-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘suddengains-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
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installed size is 102.4Mb
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installed size is  7.7Mb
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    R      1.2Mb
    data   1.9Mb
    doc    3.3Mb
installed size is 16.3Mb
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    libs  14.6Mb
installed size is  8.3Mb
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    help   1.0Mb
    libs   6.6Mb
installed size is 40.0Mb
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installed size is  5.6Mb
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    fonts   1.7Mb
    libs    3.8Mb
installed size is 10.4Mb
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    libs  10.0Mb
installed size is  6.7Mb
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    R      1.3Mb
    libs   4.5Mb
installed size is 12.1Mb
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    libs  11.3Mb
installed size is 12.3Mb
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installed size is 37.8Mb
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    doc    1.4Mb
    libs  36.0Mb
installed size is 14.4Mb
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    libs  10.2Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.4Mb
installed size is  6.3Mb
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    libs      1.5Mb
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installed size is 301.7Mb
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    libs  298.1Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
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    libs       6.6Mb
    tessdata  14.1Mb
Packages suggested but not available for checking: 'lpsymphony', 'gurobi'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.9Mb
    libs   4.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Running ‘testthat.R’ [25s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: $ operator is invalid for atomic vectors
  Backtrace:
      █
   1. └─thankr::shoulders("library") test-shoulders.R:17:2
   2.   └─thankr:::library_shoulders()
   3.     └─thankr:::build_package_list(utils::installed.packages()[, 1])
   4.       ├─thankr:::format_pkg_df(...)
   5.       │ └─base::stopifnot(is.list(lpkgs))
   6.       └─base::lapply(...)
   7.         └─thankr:::FUN(X[[i]], ...)
   8.           └─thankr:::get_maintainer(x)
  
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 9 ]
  Error: Test failures
  Execution halted
installed size is 46.8Mb
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    libs  46.4Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs    10.0Mb
    tiledb  18.6Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    libs  31.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package required but not available: ‘qpgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 133.5Mb
  sub-directories of 1Mb or more:
    R       4.5Mb
    help    1.4Mb
    libs  127.1Mb
Error(s) in re-building vignettes:
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

The following object is masked from 'package:base':

    append

Source : http://tile.stamen.com/toner/13/4056/2748.png
Source : http://tile.stamen.com/toner/13/4057/2748.png
Source : http://tile.stamen.com/toner/13/4056/2749.png
Source : http://tile.stamen.com/toner/13/4057/2749.png
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

The following object is masked from 'package:base':

    append

Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Loading required package: splines
Loading required package: Matrix
Loading required package: fds
Loading required package: rainbow
Loading required package: MASS
Loading required package: pcaPP
Loading required package: RCurl

Attaching package: 'fda'

The following object is masked from 'package:graphics':

    matplot

--- finished re-building 'trackeR.Rnw'

SUMMARY: processing the following file failed:
  ‘TourDetrackeR.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 48.6Mb
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    libs  46.6Mb
installed size is  6.1Mb
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installed size is 100.0Mb
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    doc    3.8Mb
    libs  95.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘choropleth_maps_with_tricolore.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 128-137 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘choropleth_maps_with_tricolore.Rmd’

SUMMARY: processing the following file failed:
  ‘choropleth_maps_with_tricolore.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 39.6Mb
  sub-directories of 1Mb or more:
    libs  39.0Mb
Package suggested but not available for checking: ‘TSodbc’
Package unavailable to check Rd xrefs: ‘TSodbc’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
> z <- TSget("ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT", 
+     eurostat)
May 26, 2021 7:30:39 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest
May 26, 2021 7:30:40 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: Internal Server Error

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

> user <- Sys.getenv("MYSQL_USER")

> setup <- RMySQL::dbConnect(RMySQL::MySQL(), dbname = "test")

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted

  ‘Guide.Stex’... failed
  ‘GuideAppendix.Stex’... failed
  ‘GuideDevel.Stex’... [0s/0s] OK
installed size is 10.0Mb
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    data   1.2Mb
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installed size is  8.6Mb
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    libs   2.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Plotting_Time_Series.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 39-44 (Plotting_Time_Series.Rmd) 
Error: processing vignette 'Plotting_Time_Series.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Plotting_Time_Series.Rmd’

SUMMARY: processing the following file failed:
  ‘Plotting_Time_Series.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  frame.c:147:21: warning: result of comparison of constant 4 with expression of type 'enum mad_layer' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/tuneR.Rcheck/00install.out’ for details.
installed size is 54.2Mb
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    R      1.4Mb
    libs  52.1Mb
installed size is 14.4Mb
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    libs  14.0Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       23.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/udunits2.Rcheck/00install.out’ for details.
installed size is 273.6Mb
  sub-directories of 1Mb or more:
    data       2.0Mb
    extdata    2.3Mb
    libs     269.0Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs  37.9Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  22.5Mb
installed size is  6.3Mb
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    libs   5.3Mb
installed size is 269.6Mb
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    extdata    1.1Mb
    libs     267.9Mb
installed size is  8.3Mb
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    libs   7.6Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help   2.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.0Mb
installed size is 54.6Mb
  sub-directories of 1Mb or more:
    libs  54.3Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  33.2Mb
Error(s) in re-building vignettes:
--- re-building ‘CDISC_ADaM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘CDISC_ADaM.Rmd’

--- re-building ‘Consort_flow_diagram.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Consort_flow_diagram.Rmd’

--- re-building ‘Styling_KM_plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Styling_KM_plots.Rmd’

--- re-building ‘Time_to_event_analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 101-105 (Time_to_event_analysis.Rmd) 
Error: processing vignette 'Time_to_event_analysis.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Time_to_event_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘Time_to_event_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘gg_vistime-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
--- finished re-building ‘gg_vistime-vignette.Rmd’

--- re-building ‘hc_vistime-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 34-41 (hc_vistime-vignette.Rmd) 
Error: processing vignette 'hc_vistime-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘hc_vistime-vignette.Rmd’

--- re-building ‘vistime-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 32-40 (vistime-vignette.Rmd) 
Error: processing vignette 'vistime-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘vistime-vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘hc_vistime-vignette.Rmd’ ‘vistime-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘introduction.Rmd’

--- re-building ‘shiny-example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 61-63 (shiny-example.Rmd) 
Error: processing vignette 'shiny-example.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘shiny-example.Rmd’

SUMMARY: processing the following file failed:
  ‘shiny-example.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 56.1Mb
  sub-directories of 1Mb or more:
    libs  55.7Mb
installed size is 68.2Mb
  sub-directories of 1Mb or more:
    libs  66.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   5.5Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(webex)
  > 
  > test_check("webex")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-compilation.R:16:3): minimal compile ────────────────────────────
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Backtrace:
      █
   1. └─rmarkdown::render(tf, quiet = TRUE) test-compilation.R:16:2
   2.   └─rmarkdown::pandoc_available(required_pandoc, error = TRUE)
   3.     └─rmarkdown:::stop2(paste(msg, collapse = " "))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 31 ]
  Error: Test failures
  Execution halted
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Package required but not available: ‘GO.db’

Packages suggested but not available for checking:
  'org.Hs.eg.db', 'org.Mm.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Error(s) in re-building vignettes:
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning: Removed 10 rows containing non-finite values (stat_smooth).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 5 row(s) containing missing values (geom_path).
Warning: Removed 10 rows containing missing values (geom_point).

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 214-234 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.6Mb
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/x13binary.Rcheck/00install.out’ for details.
Running examples in ‘xfun-Ex.R’ failed
The error most likely occurred in:

> ### Name: session_info
> ### Title: An alternative to sessionInfo() to print session information
> ### Aliases: session_info
> 
> ### ** Examples
> 
> xfun::session_info()
Error in packageVersion(p) : there is no package called ‘stringi’
Calls: <Anonymous> -> version_info -> lapply -> FUN -> packageVersion
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘xfun.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'xfun.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘xfun.Rmd’

SUMMARY: processing the following file failed:
  ‘xfun.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 41.6Mb
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    libs  40.7Mb
installed size is  6.3Mb
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    libs   5.9Mb
installed size is  8.7Mb
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    exampleData   1.6Mb
    libs          5.4Mb
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs      2.0Mb
installed size is 27.6Mb
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    libs  25.6Mb
installed size is 43.1Mb
  sub-directories of 1Mb or more:
    libs  42.7Mb
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.5Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.7Mb
    pictures   2.1Mb
Running 'testthat.R' [19m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ALA4R)
  `ALA4R` is deprecated and will be removed from CRAN at the end of 2021. The package to replace `ALA4R``,
  `galah`, is now available (https://CRAN.R-project.org/package=galah). For an introduction to `galah`,
  visit the GitHub page (https://github.com/AtlasOfLivingAustralia/galah).
  > 
  > ## run each test with and without caching
  > check_caching <- function(f) {
  +     ala_config(caching = "off")
  +     f()
  +     ala_config(caching = "on")
  +     f()
  +     f()
  + }
  > 
  > test_check("ALA4R")
  == Skipped tests ===============================================================
  * Broken by infrastructure upgrade (9)
  * On CRAN (189)
  * Slow test (18)
  * Unreliable web service (6)
  * skipping really slow field_info test (3)
  
  == Failed tests ================================================================
  -- Error (test-occurrences_plot.R:6:5): occurrences plot creates a plot  -------
  Error: HTTP status code 502 received.
    Either there was an error with the
                                         request, or the servers may be down
                                         (try again later). If this problem persists please notify the ALA4R
              maintainers by lodging an issue at
              https://github.com/AtlasOfLivingAustralia/ALA4R/issues/
              or emailing support@ala.org.au
  Backtrace:
      x
   1. \-ALA4R::occurrences(...) test-occurrences_plot.R:6:4
   2.   \-ALA4R:::cached_get(...)
   3.     \-ALA4R:::download_to_file(...)
   4.       \-ALA4R:::check_status_code(...)
  
  [ FAIL 1 | WARN 0 | SKIP 225 | PASS 59 ]
  Error: Test failures
  Execution halted