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

> ### Name: bundle
> ### Title: Identify bundle items that occur around a given event
> ### Aliases: bundle
> 
> ### ** Examples
> 
> library(data.table)
> temp <- as.data.table(vitals[VARIABLE == "TEMPERATURE"])
> pulse <- as.data.table(vitals[VARIABLE == "PULSE"])
> resp <- as.data.table(vitals[VARIABLE == "RESPIRATORY_RATE"])
> 
> temp[, RECORDED_TIME := as.POSIXct(RECORDED_TIME,
+   format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")]
> pulse[, RECORDED_TIME := as.POSIXct(RECORDED_TIME,
+   format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")]
> resp[, RECORDED_TIME := as.POSIXct(RECORDED_TIME,
+   format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")]
> 
> # Pass single window_hours_pre
> # All instances of bundle items within time window of event
> bundle(temp, pulse, resp,
+     bundle_names = c("PLATELETS", "INR"), window_hours_pre = 24,
+     window_hours_post = c(6, 6), join_key = "PAT_ID",
+     time_var = "RECORDED_TIME", event_name = "CREATININE", mult = "all")
Error in as.POSIXct.numeric(e) : 'origin' must be supplied
Calls: bundle ... unlist -> lapply -> FUN -> as.POSIXct -> as.POSIXct.numeric
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   16. base:::FUN(X[[i]], ...)
   18. base::as.POSIXct.numeric(e)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 94 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 7 ]
  1. Error: bundle produces expected values for test patient (@test-bundle.R#43) 
  2. Error: bundle names assign properly (@test-bundle.R#130) 
  3. Error: event name assigns properly (@test-bundle.R#162) 
  4. Error: window hours roll over (@test-bundle.R#173) 
  5. Error: default arguments function properly (@test-bundle.R#209) 
  6. Error: value change produces expected values for test patient (@test-value_change.R#25) 
  7. Error: default arguments function properly (@test-value_change.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘identify_sepsis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-76 (identify_sepsis.Rmd) 
Error: processing vignette 'identify_sepsis.Rmd' failed with diagnostics:
'origin' must be supplied
--- failed re-building ‘identify_sepsis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 59.0Mb
  sub-directories of 1Mb or more:
    libs  57.8Mb
Warning: parse error in file 'corrplot-Ex.R':
117:31: unexpected '>'
116: if(getRversion() >= '4.1.0') {
117:   corrplot(M, order = 'AOE') |>
                                   ^
Running examples in ‘corrplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: corrRect
> ### Title: Draw rectangle(s) on the correlation matrix graph.
> ### Aliases: corrRect
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(mtcars)
> M = cor(mtcars)
> 
> r = rbind(c('gear', 'wt', 'qsec', 'carb'),
+         c('wt', 'gear', 'carb', 'qsec'))
> corrplot(M, order = 'AOE') -> p
> corrRect(p, namesMat = r)
> 
> # same as using pipe operator `|>`
> if(getRversion() >= '4.1.0') {
+   corrplot(M, order = 'AOE') |> corrRect(namesMat = r)
Error: unexpected '>' in:
"if(getRversion() >= '4.1.0') {
  corrplot(M, order = 'AOE') |>"
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corrplot)
  corrplot 0.90 loaded
  > 
  > test_check('corrplot')
  Error in parse(con, n = -1, srcfile = srcfile, encoding = "UTF-8") : 
    test-corrRect.R:17:52: unexpected '>'
  16:     r = c('gear', 'wt', 'qsec', 'carb')
  17:     corrplot(M, method = 'circle', order = 'AOE') |>
                                                         ^
  Calls: test_check ... doWithOneRestart -> force -> lapply -> FUN -> source_file -> parse
  Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.4Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘covid19dbcand.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-71 (covid19dbcand.Rmd) 
Error: processing vignette 'covid19dbcand.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘covid19dbcand.Rmd’

SUMMARY: processing the following file failed:
  ‘covid19dbcand.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/cplexAPI.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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘clusterProfiler’
Running ‘testthat.R’ [24s/24s]
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 36 | SKIP 0 | PASS 144 ]
  Error: Test failures
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
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) and/or pandoc-citeproc 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:
cannot open the connection
--- failed re-building ‘cycling_data_analysis.Rmd’

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

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

> ### Name: Cylcop
> ### Title: Distribution, Density, and Random Number Generation for
> ###   Circular-Linear Copulas'
> ### Aliases: Cylcop rcylcop pcylcop dcylcop dcylcop,matrix,Copula-method
> ###   rcylcop,numeric,Copula-method pcylcop,matrix,Copula-method
> ###   rcylcop,numeric,cyl_cubsec-method dcylcop,matrix,cyl_cubsec-method
> ###   pcylcop,matrix,cyl_cubsec-method rcylcop,numeric,cyl_quadsec-method
> ###   dcylcop,matrix,cyl_quadsec-method pcylcop,matrix,cyl_quadsec-method
> ###   rcylcop,numeric,cyl_rect_combine-method
> ###   dcylcop,matrix,cyl_rect_combine-method
> ###   pcylcop,matrix,cyl_rect_combine-method
> ###   rcylcop,numeric,cyl_rot_combine-method
> ###   dcylcop,matrix,cyl_rot_combine-method
> ###   pcylcop,matrix,cyl_rot_combine-method
> ###   rcylcop,numeric,cyl_vonmises-method
> ###   dcylcop,matrix,cyl_vonmises-method pcylcop,matrix,cyl_vonmises-method
> 
> ### ** Examples
> 
> set.seed(123)
> 
> cop <- cyl_quadsec(0.1)
> rcylcop(5, cop)
             u          v
[1,] 0.2875775 0.05292327
[2,] 0.7883051 0.49067679
[3,] 0.4089769 0.92780722
[4,] 0.8830174 0.43677419
[5,] 0.9404673 0.32774987
> pcylcop(c(0.3, 0.1), cop)
[1] 0.03855951
> pcylcop(rbind(c(0.3, 0.1), c(0.2, 1)), cop)
[1] 0.03855951 0.20000000
> 
> cop <- cyl_rot_combine(copula::frankCopula(2), shift = TRUE)
Frank copula made periodic in u, by taking arithmetic mean with 90 degree rotated Frank copula

> dcylcop(u = rbind(c(0.1, 0.4), c(1.0, 0.2)), copula = cop)
Error in validObject(.Object) : 
  invalid class “mixWeights” object: superclass "Mnumeric" not defined in the environment of the object's class
Calls: dcylcop ... asMethod -> new -> initialize -> initialize -> validObject
Execution halted
installed size is 58.7Mb
  sub-directories of 1Mb or more:
    libs  57.7Mb
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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.
Warning in normalizePath(f2) :
  path[1]="webshot42ce5d62669.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot42ce5d62669.png': No such file or directory
Quitting from lines 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘data.tree.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 52.5Mb
  sub-directories of 1Mb or more:
    libs  52.1Mb
installed size is 24.8Mb
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    libs  24.7Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 97-98 (delayed.Rmd) 
Error: processing vignette 'delayed.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘delayed.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 77.3Mb
  sub-directories of 1Mb or more:
    libs  74.6Mb
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  35.8Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.9Mb
installed size is 57.6Mb
  sub-directories of 1Mb or more:
    libs  57.0Mb
Error(s) in re-building vignettes:
--- re-building ‘Part_1_Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Part_1_Introduction.Rmd’

--- re-building ‘Part_2_Transition_Densities.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 176-185 (Part_2_Transition_Densities.Rmd) 
Error: processing vignette 'Part_2_Transition_Densities.Rmd' failed with diagnostics:
there is no package called 'DiffusionRgqd'
--- failed re-building ‘Part_2_Transition_Densities.Rmd’

--- re-building ‘Part_3_Bivariate_Diffusions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Part_3_Bivariate_Diffusions.Rmd’

--- re-building ‘DiffusionRjgqd_Paper.pdf.asis’ using asis
--- finished re-building ‘DiffusionRjgqd_Paper.pdf.asis’

--- re-building ‘DiffusionRjgqd_RepMaterials.html.asis’ using asis
--- finished re-building ‘DiffusionRjgqd_RepMaterials.html.asis’

--- re-building ‘Part_4_Likelihood_Inference.html.asis’ using asis
--- finished re-building ‘Part_4_Likelihood_Inference.html.asis’

SUMMARY: processing the following file failed:
  ‘Part_2_Transition_Densities.Rmd’

Error: Vignette re-building failed.
Execution halted
Output for data("exHartigan", package = "diptest"):
  'exHartigan' data is identical to 'statfaculty' and hence deprecated.
   Use the 'statfaculty' instead
Package required but not available: ‘TSCAN’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/do.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc 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
`summarise()` ungrouping output (override with `.groups` argument)
Selecting by Total
`summarise()` ungrouping output (override with `.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.
Warning in normalizePath(f2) :
  path[1]="webshot14cc2fa555ba.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot14cc2fa555ba.png': No such file or directory
Quitting from lines 136-155 (DSjobtracker.Rmd) 
Error: processing vignette 'DSjobtracker.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘DSjobtracker.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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) and/or pandoc-citeproc 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:
cannot open the connection
--- failed re-building ‘Designing-33PC.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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    doc    2.6Mb
    libs   5.3Mb
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  24.1Mb
Package suggested but not available for checking: ‘TSA’
Package unavailable to check Rd xrefs: ‘dixon’
Error: package or namespace load failed for ‘echarty’:
 .onLoad failed in loadNamespace() for 'echarty', details:
  call: loadNamespace(name)
  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.
installed size is 77.0Mb
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    libs  76.2Mb
installed size is 84.9Mb
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installed size is 17.1Mb
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    libs  14.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.2Mb
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/4.0/emstreeR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘epanet2toolkit’
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: `tbl_df()` is deprecated as of 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.
Warning in normalizePath(f2) :
  path[1]="webshot783155a38ab4.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot783155a38ab4.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
--- 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: `tbl_df()` is deprecated as of 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 ‘epiflows-class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 105.1Mb
  sub-directories of 1Mb or more:
    libs  103.3Mb
Running ‘test-all.R’ [3s/5s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  [1] 5 - 4 == 1
  
  ── 4. Failure: ggplot2 plots in a single expression are captured (@test-graphics
  `x` not equal to `expected`.
  Lengths differ: 5 is not 4
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 49 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: ggplot is captured (@test-graphics.r#13) 
  2. Failure: ggplot is captured (@test-graphics.r#15) 
  3. Failure: ggplot2 plots in a single expression are captured (@test-graphics.r#47) 
  4. Failure: ggplot2 plots in a single expression are captured (@test-graphics.r#49) 
  
  Error: testthat unit tests failed
  Execution halted
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/4.0/ExomeDepth.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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 42.4Mb
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    libs  42.2Mb
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    libs   9.1Mb
installed size is  8.7Mb
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installed size is 72.2Mb
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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) and/or pandoc-citeproc 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
Package suggested but not available for checking: ‘ExtDist’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   3.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro-flashCard.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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:
cannot open the connection
--- failed re-building ‘Intro-flashCard.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 73.9Mb
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installed size is 20.5Mb
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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) and/or pandoc-citeproc 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:
polygon edge not found
--- failed re-building ‘Using_fontHind.Rmd’

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

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) and/or pandoc-citeproc 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:
polygon edge not found
--- failed re-building ‘Using_fontMPlus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/fRLR.Rcheck/00install.out’ for details.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
cannot open the connection
--- 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) and/or pandoc-citeproc 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
Package required but not available: ‘KEGGREST’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘GALLO.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 45-59 (GALLO.Rmd) 
Error: processing vignette 'GALLO.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘GALLO.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   9.5Mb
installed size is 68.2Mb
  sub-directories of 1Mb or more:
    libs  67.8Mb
installed size is 59.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     56.0Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.8Mb
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/4.0/GENLIB.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R         8.9Mb
    extdata   1.6Mb
Package required but not available: ‘cqn’

Packages suggested but not available for checking:
  'ChAMP', 'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/ggbreak.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggBubbles.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: knitr
Loading required package: ggplot2
Loading required package: ggBubbles
Quitting from lines 30-40 (ggBubbles.Rmd) 
Error: processing vignette 'ggBubbles.Rmd' failed with diagnostics:
could not find function "CRANpkg"
--- failed re-building ‘ggBubbles.Rmd’

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

Error: Vignette re-building failed.
Execution halted
make_gradient_fill: no visible binding for global variable
  ‘linearGradient’
Undefined global functions or variables:
  linearGradient
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) and/or pandoc-citeproc 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.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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.
Warning in normalizePath(f2) :
  path[1]="webshotf75d53bfa25a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotf75d53bfa25a.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- 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) and/or pandoc-citeproc 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
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) and/or pandoc-citeproc 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.
Quitting from lines 185-186 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 49.6Mb
  sub-directories of 1Mb or more:
    libs  48.9Mb
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
Running ‘AAAtest-all.R’ [55s/55s]
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 1.3.2
  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 12.9Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R   6.3Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 243-244 (gprofiler2.Rmd) 
Error: processing vignette 'gprofiler2.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘gprofiler2.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required and available but unsuitable versions: 'datasets', 'grid'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
create_gradient_as_geometry: no visible global function definition for
  ‘linearGradient’
create_gradient_as_geometry: no visible global function definition for
  ‘radialGradient’
Undefined global functions or variables:
  linearGradient radialGradient
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-34 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘profiling.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘run-tests.R’ [3s/6s]
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$new(toolkit, from, to, by, value, horizontal, handler,     action, container, ...)
   8: .gslider.guiWidgetsToolkitRGtk2(toolkit, from, to, by, value,     horizontal, handler, action, container = container, ...)
   9: .gslider(toolkit, from, to, by, value, horizontal, handler, action,     container = container, ...)
  10: gslider(from = 0, to = 100, by = 1, cont = g)
  11: eval(ei, envir)
  12: eval(ei, envir)
  13: withVisible(eval(ei, envir))
  14: source(i)
  15: FUN(X[[i]], ...)
  16: lapply(X = X, FUN = FUN, ...)
  17: sapply(f, function(i) {    message("testing ", i)    source(i)})
  An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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:
cannot open the connection
--- 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 ‘Basic_use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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:
cannot open the connection
--- failed re-building ‘Basic_use.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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/high-sierra-x86_64/results/4.0/hdf5r.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/HierO.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hpackedbubble.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 59.3Mb
  sub-directories of 1Mb or more:
    libs  58.8Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hwordcloud.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.5Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ibmsunburst.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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) and/or pandoc-citeproc 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
Package unavailable to check Rd xrefs: ‘ridge’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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) and/or pandoc-citeproc 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
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.
Warning in normalizePath(f2) :
  path[1]="webshota3e06b28a5bc.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshota3e06b28a5bc.png': No such file or directory
Quitting from lines 32-34 (IntGraphTutorial.Rmd) 
Error: processing vignette 'IntGraphTutorial.Rmd' failed with diagnostics:
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--- failed re-building ‘IntGraphTutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Package suggested but not available for checking: ‘iNZightPlots’
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) and/or pandoc-citeproc 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) 
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--- 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
Namespace in Imports field not imported from: ‘timereg’
  All declared Imports should be used.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          15.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
Running examples in ‘KernelICA-Ex.R’ failed
The error most likely occurred in:

> ### Name: kernel_ica
> ### Title: Kernel Independent Component Analysis
> ### Aliases: kernel_ica
> 
> ### ** Examples
> 
> require(JADE)
Loading required package: JADE
> require(ICtest)
Loading required package: ICtest
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: ggplot2
> 
> n <- 2000
> p <- 3
> S <- matrix(0, n, p)
> 
> # the three data sources used in this example
> S[, 1] <- rexp(n, rate = 0.4)
> S[, 2] <- runif(n, 2, 4)
> S[, 3] <- rt(n, 5)
> 
> W <- ICtest::rorth(p) # creates an orthogonal matrix
> y <- S %*% t(W) # mixes the data
> 
> # applying kernel ICA method
> res <- KernelICA::kernel_ica(y, variant = "kgv", kernel = "hermite")

 *** caught segfault ***
address 0x0, cause 'unknown'

Traceback:
 1: ManifoldOptim::manifold.optim(prob, mani.defn, method = optim_method,     mani.params = mani_params, solver.params = solver_params,     x0 = t(init[[i]]))
 2: KernelICA::kernel_ica(y, variant = "kgv", kernel = "hermite")
An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/kmcudaR.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc 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
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘LDATS_codebase.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘LDATS_codebase.Rmd’

--- re-building ‘paper-comparison.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 59-60 (paper-comparison.Rmd) 
Error: processing vignette 'paper-comparison.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘paper-comparison.Rmd’

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

SUMMARY: processing the following file failed:
  ‘paper-comparison.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) and/or pandoc-citeproc 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 CRS 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 CRS definition
Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
  Discarded ellps WGS 84 in CRS 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 CRS definition
Warning in normalizePath(f2) :
  path[1]="webshot155cc2c57d3d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot155cc2c57d3d.png': No such file or directory
Quitting from lines 32-38 (usage-leaflet.Rmd) 
Error: processing vignette 'usage-leaflet.Rmd' failed with diagnostics:
cannot open the connection
--- 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) and/or pandoc-citeproc 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
Packages required and available but unsuitable versions: 'rstan', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.5Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [11s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_parsers.R:101:3): OceanOptics others ────────────────────────────
  Error: argument is of length zero
  Backtrace:
      █
   1. ├─testthat::expect_known_hash(...) test_parsers.R:101:2
   2. │ └─testthat::quasi_label(enquo(object), arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─base::suppressWarnings(...)
   5. │ └─base::withCallingHandlers(...)
   6. └─lightr::lr_parse_jaz(test.file("non_english", "OceanView_nonEN.txt"))
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 513 ]
  Error: Test failures
  Execution halted
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘linkspotterVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 56.9Mb
  sub-directories of 1Mb or more:
    libs  56.0Mb
installed size is 51.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  49.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘lspline.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 18-23 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘lspline.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.3Mb
Package required but not available: ‘ssize’

Packages suggested but not available for checking:
  'GEOmetadb', 'KEGGREST', 'KEGGgraph', 'pdInfoBuilder', 'lumi',
  'simpleaffy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs         14.8Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.9Mb
Package suggested but not available for checking: ‘flare’
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  11.4Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.3.3     ✔ purrr   0.3.4
✔ tibble  3.1.0     ✔ dplyr   1.0.5
✔ 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.
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  8.8Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.6Mb
installed size is 89.2Mb
  sub-directories of 1Mb or more:
    libs  88.5Mb
Packages required but not available: 'KEGGREST', 'ChemmineR', 'Rdisop'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'annaffy', 'hgu133plus2.db', 'hgu95av2.db'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.7Mb
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    5.4Mb
    libs  19.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Package suggested but not available for checking: ‘BSgenome.Mmusculus.UCSC.mm10’
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/4.0/microsimulation.Rcheck/00install.out’ for details.
Running examples in ‘migest-Ex.R’ failed
The error most likely occurred in:

> ### Name: index_distance
> ### Title: Summary indices of migration distance
> ### Aliases: index_distance
> 
> ### ** Examples
> 
> # single year
> index_distance(
+   m = subset(korea_reg, year == 2020), 
+   d = korea_dist
+ )
Error in index_distance(m = subset(korea_reg, year == 2020), d = korea_dist) : 
  different region names in m and d
Execution halted
installed size is 101.3Mb
  sub-directories of 1Mb or more:
    libs  100.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   1.6Mb
installed size is 340.0Mb
  sub-directories of 1Mb or more:
    libs  339.6Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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 10.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.0Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 302-305 (international-mortality-tables-overview.Rmd) 
Error: processing vignette 'international-mortality-tables-overview.Rmd' failed with diagnostics:
object 'EttlPagler.male' 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) and/or pandoc-citeproc 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  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.6Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 119-120 (UsageOfMrSGUIDE.Rmd) 
Error: processing vignette 'UsageOfMrSGUIDE.Rmd' failed with diagnostics:
cannot open the connection
--- 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 ‘msaR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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.
Quitting from lines 25-32 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
cannot open the connection
--- 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 ‘msir.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot133ae6439653f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot133ae6439653f.png': No such file or directory
Quitting from lines 101-103 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  17.6Mb
Running examples in ‘mssqlR-Ex.R’ failed
Package suggested but not available for checking: ‘switchBox’
installed size is 104.2Mb
  sub-directories of 1Mb or more:
    doc    5.9Mb
    libs  97.1Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/4s]
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  6.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.2Mb
Package required and available but unsuitable version: ‘rhdf5’

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

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/high-sierra-x86_64/results/4.0/nloptr.Rcheck/00install.out’ for details.
installed size is 85.7Mb
  sub-directories of 1Mb or more:
    libs  85.2Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
Package suggested but not available for checking: ‘vcfR’
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/OpenCL.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc 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:
cannot open the connection
--- failed re-building ‘openland_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘org.At.tair.db’
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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:
cannot open the connection
--- failed re-building ‘progressive_packing.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘packClassic’
Packages suggested but not available for checking:
  'org.Dr.eg.db', 'p2data', 'scde'
installed size is 56.7Mb
  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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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

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 ‘introduction-to-parallelplot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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:
cannot open the connection
--- 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 ‘introduction-to-parcoords-.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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:
cannot open the connection
--- 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  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.9Mb
Packages required but not available: 'KEGGREST', 'KEGGgraph'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/pbdPROF.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/pcaL1.Rcheck/00install.out’ for details.
installed size is 105.6Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
    libs  102.1Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
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) and/or pandoc-citeproc 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.
Warning in normalizePath(f2) :
  path[1]="webshot15ff6fc93f26.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot15ff6fc93f26.png': No such file or directory
Quitting from lines 93-133 (pdxTrees-vignette.Rmd) 
Error: processing vignette 'pdxTrees-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘pdxTrees-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/permGPU.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.9Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot13f536e690bac.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot13f536e690bac.png': No such file or directory
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
cannot open the connection
--- 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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   9.5Mb
Running examples in ‘plfMA-Ex.R’ failed
The error most likely occurred in:

> ### Name: plfMA
> ### Title: A function to launch the plfMA GUI.
> ### Aliases: plfMA
> ### Keywords: GUI
> 
> ### ** Examples
> 
> x<-matrix(1:100,ncol=10)
> plfMA(x)
Loading required package: gWidgets2RGtk2
Loading required package: memoise
Loading required package: RGtk2
Loading required package: gWidgets2
Loading required package: digest

 *** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: .RGtkCall("S_gtk_widget_set_visible", object, visible, PACKAGE = "RGtk2")
 2: method(obj, ...)
 3: widget$setVisible(as.logical(value))
 4: obj$set_visible(as.logical(value))
 5: `visible<-.default`(`*tmp*`, value = TRUE)
 6: `visible<-`(`*tmp*`, value = TRUE)
 7: plfMA(x)
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘about-podr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 42-64 (about-podr.Rmd) 
Error: processing vignette 'about-podr.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘about-podr.Rmd’

SUMMARY: processing the following file failed:
  ‘about-podr.Rmd’

Error: Vignette re-building failed.
Execution halted
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot15e404e0de3dd.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot15e404e0de3dd.png': No such file or directory
Quitting from lines 130-131 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PPQplan-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required and available but unsuitable version: ‘parallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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) and/or pandoc-citeproc 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:
cannot open the connection
--- failed re-building ‘predict3d.Rmd’

SUMMARY: processing the following file failed:
  ‘predict3d.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 14.0Mb
  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) and/or pandoc-citeproc 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
Warning in normalizePath(f2) :
  path[1]="webshot26ff63ed64f9.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot26ff63ed64f9.png': No such file or directory
Quitting from lines 43-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
--- 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PRISMA.Rmd’

--- re-building ‘exclusionflowcharts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 25-31 (exclusionflowcharts.Rmd) 
Error: processing vignette 'exclusionflowcharts.Rmd' failed with diagnostics:
cannot open the connection
--- 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 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Package suggested but not available for checking: ‘dm’
Package unavailable to check Rd xrefs: ‘dm’
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    libs  46.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   3.0Mb
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Package required but not available: ‘muscle’

Package suggested but not available for checking: ‘KEGGREST’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 161-162 (PWFSLSmoke.Rmd) 
Error: processing vignette 'PWFSLSmoke.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PWFSLSmoke.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 70.8Mb
  sub-directories of 1Mb or more:
    libs  70.4Mb
Error(s) in re-building vignettes:
--- re-building ‘qqr_Package.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: xml2
Loading required package: rvest
Loading required package: tidyverse
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.3.2     ✔ purrr   0.3.4
✔ tibble  3.0.4     ✔ dplyr   1.0.2
✔ tidyr   1.1.2     ✔ stringr 1.4.0
✔ readr   1.4.0     ✔ forcats 0.5.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter()         masks stats::filter()
✖ readr::guess_encoding() masks rvest::guess_encoding()
✖ dplyr::lag()            masks stats::lag()
✖ purrr::pluck()          masks rvest::pluck()
Quitting from lines 33-34 (qqr_Package.Rmd) 
Error: processing vignette 'qqr_Package.Rmd' failed with diagnostics:
LibreSSL SSL_connect: SSL_ERROR_SYSCALL in connection to especiais.gazetadopovo.com.br:443 
--- failed re-building ‘qqr_Package.Rmd’

SUMMARY: processing the following file failed:
  ‘qqr_Package.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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- 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 ‘wilcox1973.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.5Mb
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated

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

Probably some imports need to be declared in the NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_r_symbols.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'introduction_r_symbols.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘introduction_r_symbols.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-66 (r3dmol.Rmd) 
Error: processing vignette 'r3dmol.Rmd' failed with diagnostics:
invalid 'path' argument
--- 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) and/or pandoc-citeproc 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:
invalid 'path' argument
--- failed re-building ‘style-functions.Rmd’

SUMMARY: processing the following files failed:
  ‘r3dmol.Rmd’ ‘style-functions.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Running ‘testthat.R’ [42s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  $ operator is invalid for atomic vectors
  Backtrace:
   1. testthat::expect_true(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(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 85 | SKIPPED: 3 | WARNINGS: 4 | FAILED: 1 ]
  1. Error: Listing of Rapporteket packages is present (@test-miscellaneous-functions.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required and available but unsuitable versions:
  'GenomicRanges', 'IRanges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    libs   6.6Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   7.6Mb
installed size is 41.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  38.8Mb
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/Rblpapi.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc 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
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/Rcplex.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/4.0/RcppClassic.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/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/4.0/RcppMLPACK.Rcheck/00install.out’ for details.
installed size is 41.4Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      28.0Mb
    libs     11.5Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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/4.0/RDieHarder.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 157-163 (ReDaMoR.Rmd) 
Error: processing vignette 'ReDaMoR.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ReDaMoR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.4Mb
Running ‘testthat.R’ [6s/21s]
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 ‘log_parsing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'log_parsing.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘log_parsing.Rmd’

--- re-building ‘url_parsing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'url_parsing.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘url_parsing.Rmd’

SUMMARY: processing the following files failed:
  ‘log_parsing.Rmd’ ‘url_parsing.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/rGEDI.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
sh: line 1: 32693 Abort trap: 6           '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpO7mEFg/file7fb03604f57d' 2>&1 < '/Volumes/Temp/tmp/RtmpO7mEFg/file7fb07f90fd3f'
--- 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: 32730 Abort trap: 6           '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpO7mEFg/file7fb065ae35eb' 2>&1 < '/Volumes/Temp/tmp/RtmpO7mEFg/file7fb010560b74'
--- 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
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) and/or pandoc-citeproc 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
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/Rhpc.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/4.0/RInside.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/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 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
installed size is 54.5Mb
  sub-directories of 1Mb or more:
    libs  53.9Mb
Packages suggested but not available for checking: 'reactome.db', 'fgsea'
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/RMark.Rcheck/00install.out’ for details.
installed size is 69.1Mb
  sub-directories of 1Mb or more:
    libs  68.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/RmecabKo.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.9Mb
installed size is 40.4Mb
  sub-directories of 1Mb or more:
    libs  39.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/Rmpi.Rcheck/00install.out’ for details.
installed size is 96.5Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     94.4Mb
installed size is  8.0Mb
  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) and/or pandoc-citeproc 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

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 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/ROracle.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/rpanel.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rpivotTableIntroduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/Rpoppler.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/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) and/or pandoc-citeproc 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:
cannot open the connection
--- failed re-building ‘rpredictit-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/rrd.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/RSclient.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/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 26.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  24.2Mb
installed size is 177.6Mb
  sub-directories of 1Mb or more:
    R       1.6Mb
    doc     4.5Mb
    libs  170.9Mb
installed size is 35.1Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
installed size is 256.4Mb
  sub-directories of 1Mb or more:
    lib    28.7Mb
    libs  225.0Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rsyncrosim_tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 15-19 (rsyncrosim_tutorial.Rmd) 
Error: processing vignette 'rsyncrosim_tutorial.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘rsyncrosim_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.5Mb
Packages required but not available:
  'GSVAdata', 'clusterProfiler', 'rWikiPathways'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 63.2Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     58.9Mb
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/4.0/RVowpalWabbit.Rcheck/00install.out’ for details.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.8Mb
Package suggested but not available for checking: ‘org.Sc.sgd.db’
Error(s) in re-building vignettes:
  ...
--- re-building ‘sankeywheel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-44 (sankeywheel.Rmd) 
Error: processing vignette 'sankeywheel.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sankeywheel.Rmd’

SUMMARY: processing the following file failed:
  ‘sankeywheel.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.
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'MAST', 'monocle'
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   7.7Mb
Missing or unexported objects:
  ‘SingleCellExperiment::mainExpName’
  ‘SingleCellExperiment::mainExpName<-’
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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.
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 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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
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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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’

Package suggested but not available for checking: ‘copynumber’

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) and/or pandoc-citeproc 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.
Quitting from lines 155-198 (simrec-vignette.Rmd) 
Error: processing vignette 'simrec-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘simrec-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  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   4.9Mb
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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.
Warning in normalizePath(f2) :
  path[1]="webshot1188ad8334a0.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1188ad8334a0.png': No such file or directory
Quitting from lines 85-86 (understanding_sortable_js.Rmd) 
Error: processing vignette 'understanding_sortable_js.Rmd' failed with diagnostics:
cannot open the connection
--- 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) and/or pandoc-citeproc 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'
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) and/or pandoc-citeproc 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, which.max, which.min

Identifing all possible orderings..
Total run time: 1.54 secs
Identifing all possible orderings..
Total run time: 0.7 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.
Warning in normalizePath(f2) :
  path[1]="webshot10bcd6cd1471f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot10bcd6cd1471f.png': No such file or directory
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.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) and/or pandoc-citeproc 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.
Warning in normalizePath(f2) :
  path[1]="webshot9895bb23bf.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot9895bb23bf.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
--- 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 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  13.3Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.0Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   9.7Mb
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.4.6)
than is installed on your system (1.0.6). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.4.6)
than is installed on your system (1.0.6). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.4.6)
than is installed on your system (1.0.6). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'MAIT', 'KEGGgraph', 'KEGGREST', 'rcytoscapejs'
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      3.6Mb
installed size is 51.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  49.8Mb
installed size is 69.7Mb
  sub-directories of 1Mb or more:
    libs  69.3Mb
Package which this enhances but not available for checking: ‘Zelig’
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:
subscript out of bounds
--- failed re-building ‘statelists.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.6Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/string2path.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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 16.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  14.5Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    apps   2.3Mb
    libs  10.4Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.6Mb
installed size is 47.3Mb
  sub-directories of 1Mb or more:
    libs  46.9Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 113-154 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘toOrdinal.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘toOrdinal.Rmd’

SUMMARY: processing the following file failed:
  ‘toOrdinal.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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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: Matrix

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 ‘structuredCoalescent.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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
installed size is 100.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  95.5Mb
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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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
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)
Jul 15, 2020 5:09:43 PM 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
Jul 15, 2020 5:09:49 PM 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
Error(s) in re-building vignettes:
--- re-building ‘Guide.Stex’ using Sweave

Error: processing vignette 'Guide.Stex' failed with diagnostics:
 chunk 3 
Error : package ‘TSdbi’ required by ‘TSsdmx’ could not be found

--- failed re-building ‘Guide.Stex’

--- 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  8.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.6Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: `arrange_()` is deprecated as of 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.
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.
Warning in normalizePath(f2) :
  path[1]="webshotcb332132ed7c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotcb332132ed7c.png': No such file or directory
Quitting from lines 39-44 (Plotting_Time_Series.Rmd) 
Error: processing vignette 'Plotting_Time_Series.Rmd' failed with diagnostics:
cannot open the connection
--- 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/4.0/tuneR.Rcheck/00install.out’ for details.
installed size is 54.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  52.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/udunits2.Rcheck/00install.out’ for details.
installed size is 254.0Mb
  sub-directories of 1Mb or more:
    data       2.0Mb
    extdata    2.3Mb
    libs     249.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘convexhull.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 93-98 (convexhull.Rmd) 
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘convexhull.Rmd’

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

Error: Vignette re-building failed.
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) and/or pandoc-citeproc 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.
Warning in normalizePath(f2) :
  path[1]="webshot15cf2fe0b0f4.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot15cf2fe0b0f4.png': No such file or directory
Quitting from lines 54-55 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘basic_usage.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 ‘intro_to_vegalite.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro_to_vegalite.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 34.4Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
Package suggested but not available for checking: ‘igraph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-visNetwork.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Introduction-to-visNetwork.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-visNetwork.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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘wordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘wordcloud.Rmd’

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

Error: Vignette re-building failed.
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) and/or pandoc-citeproc 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.
Warning in normalizePath(f2) :
  path[1]="webshot110e5d4f60a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot110e5d4f60a.png': No such file or directory
Quitting from lines 214-234 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/x13binary.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘modification.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'modification.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘modification.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
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) and/or pandoc-citeproc 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 43.5Mb
  sub-directories of 1Mb or more:
    libs  43.2Mb
installed size is 42.5Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/actuar.Rcheck/00install.out' for details.
installed size is 92.1Mb
  sub-directories of 1Mb or more:
    gdal   2.1Mb
    libs  89.5Mb
Running examples in 'arealDB-Ex.R' failed
The error most likely occurred in:

> ### Name: makeExampleDB
> ### Title: Build an example database
> ### Aliases: makeExampleDB
> 
> ### ** Examples
> 
> # to merely register a set of files
> makeExampleDB(until = "regTable")
I have created a new project directory.
  -> please run 'setVariables()' to create a translation table for territories.
please type in the path to the local folder where the licence is stored: 
Error: Cannot open file for writing:
* 'D:\temp\Rtmp238teZ\newDB\inv_dataseries.csv'
Execution halted
Warning: parse error in file 'lines':
62: unexpected '>'
40: library(ggplot2)
41: data.frame(loud = c(20, 35, 50, 65), perc = c(0,10,65,100)) |>
                                                                 ^
Running examples in 'audiometry-Ex.R' failed
The error most likely occurred in:

> ### Name: gg_freiburg
> ### Title: Freiburger Sprachtest data with ggplot2
> ### Aliases: gg_freiburg
> 
> ### ** Examples
> 
> library(ggplot2)
> data.frame(loud = c(20, 35, 50, 65), perc = c(0,10,65,100)) |>
Error: unexpected '>' in "data.frame(loud = c(20, 35, 50, 65), perc = c(0,10,65,100)) |>"
Execution halted
Warning: parse error in file 'd:/RCompile/CRANpkg/lib/4.0/audiometry/doc/Freiburger.R':
/RCompile/CRANpkg/lib/4.0/audiometry/doc/Freiburger.R:16:64: unexpected '>'
15: data.frame(loud1 = c(10, 20, 30, 40), perc1 = c(0, 25, 75, 100),
16:            loud2 = c(20, 35, 50, 65), perc2 = c(0,10,65,100)) |>
                                                                   ^
Error(s) in re-building vignettes:
--- re-building 'Freiburger.Rmd' using rmarkdown
Quitting from lines 36-43 (Freiburger.Rmd) 
Error: processing vignette 'Freiburger.Rmd' failed with diagnostics:
<text>:2:64: unexpected '>'
1: data.frame(loud1 = c(10, 20, 30, 40), perc1 = c(0, 25, 75, 100),
2:            loud2 = c(20, 35, 50, 65), perc2 = c(0,10,65,100)) |>
                                                                  ^
--- failed re-building 'Freiburger.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  wmm.c:428:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int)'} [-Wincompatible-pointer-types]
  wmm.c:429:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int,  int)'} [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0/audio.Rcheck/00install.out' for details.
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

  Natural language support but running in an English locale

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

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

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BALD.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BALLI.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.7Mb
installed size is 145.8Mb
  sub-directories of 1Mb or more:
    include  144.8Mb
Running 'testthat.R' [108s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BIGL)
  > 
  > test_check("BIGL")
  == Skipped tests ===============================================================
  * On CRAN (5)
  
  == Failed tests ================================================================
  -- Failure (test_calls.R:9:3): calls -------------------------------------------
  rs$maxR$Call not equal to "Syn".
  1/1 mismatches
  x[1]: "None"
  y[1]: "Syn"
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 157 ]
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BinQuasi.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BioVenn.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'bkmrhat-vignette.Rmd' using knitr
For guided examples, go to 'https://jenfb.github.io/bkmr/overview.html'
Loading required package: coda
Diagnostics and parallel chain functioning for Bayesian kernel machine regression
Quitting from lines 41-54 (bkmrhat-vignette.Rmd) 
Error: processing vignette 'bkmrhat-vignette.Rmd' failed with diagnostics:
Initialization of plan() failed, because the test future used for validation failed. The reason was: Package 'future' is not installed on worker (r_version: 4.0.5 (2021-03-31); platform: x86_64-w64-mingw32 (64-bit); os: Windows Server 2008 x64 build 6003, Service Pack 2; hostname: CRANWIN)
--- failed re-building 'bkmrhat-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    fonts   2.4Mb
    lib     3.4Mb
Found the following significant warnings:
  w32-backend.c:24:5: warning: initialization of 'char **' from incompatible pointer type 'const char **' [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0/Cairo.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CDSeq.Rcheck/00install.out' for details.
reg_match: no visible global function definition for 'gregexec'
Undefined global functions or variables:
  gregexec
Running examples in 'cfid-Ex.R' failed
The error most likely occurred in:

> ### Name: CounterfactualConjunction
> ### Title: Counterfactual Conjunction
> ### Aliases: CounterfactualConjunction conj
> 
> ### ** Examples
> 
> # The conjunction described in 'details'
> v1 <- cf("Y", 0)
> v2 <- cf("Y", 1, c("X" = 0))
> c1 <- conj(v1, v2)
> 
> # Alternative construction
> c1 <- v1 + v2
> 
> # Adding further variables
> v3 <- cf("X", 1)
> c2 <- c1 + v3
Warning: Incompatible methods ("+.CounterfactualConjunction", "+.CounterfactualVariable") for "+"
Error in c1 + v3 : non-numeric argument to binary operator
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ch.Rcheck/00install.out' for details.
Running examples in 'ClustAssess-Ex.R' failed
The error most likely occurred in:

> ### Name: marker_overlap
> ### Title: Cell-wise marker gene overlap
> ### Aliases: marker_overlap
> 
> ### ** Examples
> 
> suppressWarnings({
+ set.seed(12345)
+ library(Seurat)
+ 
+ # cluster with Louvain algorithm
+ pbmc_small = FindClusters(pbmc_small, resolution=0.8, verbose=FALSE)
+ 
+ # cluster with k-means
+ pbmc.pca = Embeddings(pbmc_small, 'pca')
+ pbmc_small@meta.data$kmeans_clusters = kmeans(pbmc.pca, centers=2)$cluster
+ 
+ # compare the markers
+ Idents(pbmc_small) = pbmc_small@meta.data$seurat_clusters
+ louvain.markers = FindAllMarkers(pbmc_small, logfc.threshold=1, verbose=FALSE)
+ 
+ Idents(pbmc_small) = pbmc_small@meta.data$kmeans_clusters
+ kmeans.markers = FindAllMarkers(pbmc_small, logfc.threshold=1, verbose=FALSE)
+ 
+ pbmc_small@meta.data$jsi = marker_overlap(louvain.markers, kmeans.markers,
+   pbmc_small@meta.data$seurat_clusters, pbmc_small@meta.data$kmeans_clusters)
+ 
+ # which cells have the same markers, regardless of clustering?
+ FeaturePlot(pbmc_small, 'jsi')
+ })
Error: package or namespace load failed for 'Seurat' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace 'Matrix' 1.3-2 is already loaded, but >= 1.3.3 is required
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ClustAssess.Rmd' using rmarkdown
Quitting from lines 22-27 (ClustAssess.Rmd) 
Error: processing vignette 'ClustAssess.Rmd' failed with diagnostics:
package or namespace load failed for 'Seurat' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace 'Matrix' 1.3-2 is already loaded, but >= 1.3.3 is required
--- failed re-building 'ClustAssess.Rmd'

--- re-building 'comparing-soft-and-hierarchical.Rmd' using rmarkdown
--- finished re-building 'comparing-soft-and-hierarchical.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("clustermq")
  Loading required package: clustermq
  * Option 'clustermq.scheduler' not set, defaulting to 'LOCAL'
  --- see: https://mschubert.github.io/clustermq/articles/userguide.html#configuration
  Assertion failed: nbytes == sizeof (dummy) (../zeromq-4.2.1/src/signaler.cpp:192)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/cns.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CNVScope.Rcheck/00install.out' for details.
Warning: parse error in file 'lines':
8: unexpected '>'
56: giris <- group_by(iris, Species)
57: giris |>
           ^
Running examples in 'compstatr-Ex.R' failed
The error most likely occurred in:

> ### Name: cs_load_year
> ### Title: Create Year List Object
> ### Aliases: cs_load_year
> 
> ### ** Examples
> 
> # create temporary directory
> tmpdir <- tempdir()
> fs::dir_create(paste0(tmpdir,"/data/"))
> 
> # load sample files into temporary directory
> cs_example(path = paste0(tmpdir,"/data/"))
> 
> # prep sample files
> cs_prep_year(path = paste0(tmpdir,"/data/"))
> 
> # load sample files
> yearList17 <- cs_load_year(path = paste0(tmpdir,"/data/"))
> 
> # delete data
> fs::dir_delete(paste0(tmpdir,"/data/"))
Error: [EBUSY] Failed to remove 'D:/temp/RtmpsbrrFC/data/april2017.csv': resource busy or locked
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    libs      2.0Mb
Warning: parse error in file 'corrplot-Ex.R':
118:31: unexpected '>'
117: if(getRversion() >= '4.1.0') {
118:   corrplot(M, order = 'AOE') |>
                                   ^
Running examples in 'corrplot-Ex.R' failed
The error most likely occurred in:

> ### Name: corrRect
> ### Title: Draw rectangle(s) on the correlation matrix graph.
> ### Aliases: corrRect
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(mtcars)
> M = cor(mtcars)
> 
> r = rbind(c('gear', 'wt', 'qsec', 'carb'),
+         c('wt', 'gear', 'carb', 'qsec'))
> corrplot(M, order = 'AOE') -> p
> corrRect(p, namesMat = r)
> 
> # same as using pipe operator `|>`
> if(getRversion() >= '4.1.0') {
+   corrplot(M, order = 'AOE') |> corrRect(namesMat = r)
Error: unexpected '>' in:
"if(getRversion() >= '4.1.0') {
  corrplot(M, order = 'AOE') |>"
Execution halted
Warning: parse error in file 'testthat/test-corrRect.R':
17:52: unexpected '>'
16:     r = c('gear', 'wt', 'qsec', 'carb')
17:     corrplot(M, method = 'circle', order = 'AOE') |>
                                                       ^
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(corrplot)
  corrplot 0.90 loaded
  > 
  > test_check('corrplot')
  Error in parse(con, n = -1, srcfile = srcfile, encoding = "UTF-8") : 
    test-corrRect.R:17:52: unexpected '>'
  16:     r = c('gear', 'wt', 'qsec', 'carb')
  17:     corrplot(M, method = 'circle', order = 'AOE') |>
                                                         ^
  Calls: test_check ... doWithOneRestart -> force -> lapply -> FUN -> source_file -> parse
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cplexAPI.Rcheck/00install.out' for details.
Running examples in 'crsra-Ex.R' failed
The error most likely occurred in:

> ### Name: crsra_import_course
> ### Title: Imports all the .csv files into one list consisting of all the
> ###   tables within the course.
> ### Aliases: crsra_import_course
> 
> ### ** Examples
> 
> zip_file = system.file("extdata", "fake_course_7051862327916.zip",
+ package = "crsra")
> bn = basename(zip_file)
> bn = sub("[.]zip$", "", bn)
> res = unzip(zip_file, exdir = tempdir(), overwrite = TRUE)
Error in unzip(zip_file, exdir = tempdir(), overwrite = TRUE) : 
  cannot open file 'D:/temp/RtmpIV8r98/fake_course_7051862327916/programming_submission_part_grid_grading_statuses.csv': Invalid argument
Execution halted
Running examples in 'DAISIE-Ex.R' failed
The error most likely occurred in:

> ### Name: DAISIE_plot_input
> ### Title: DAISIE tree plot
> ### Aliases: DAISIE_plot_input
> 
> ### ** Examples
> 
> 
>  # check whether package tibble has been installed
>  if (!requireNamespace('tibble', quietly = TRUE)) {
+     cat("Package tibble needed for this function to work. Please install it.")
+  } else {
+  set.seed(42)
+ 
+  # Random trees
+  t1 <- ape::rtree(10)
+  t1$tip.label <- gsub("t", "t1.", t1$tip.label)
+  t2 <- ape::rtree(3)
+  t2$tip.label <- gsub("t", "t2.", t2$tip.label)
+  t3 <- DAISIE:::DAISIE_single_branch(
+    "t3.1",
+    edge.length = 4.6
+  ) # tree with one species
+  trees <- list(t1, t2, t3)
+  names(trees) <- c("A", "B", "C")
+ 
+  # Toy colonization events for each clade
+  tcols <- c(4.5, 5, 4.6)
+ 
+  # Toy metadata
+  metadata <- tibble::tibble(
+    clade = names(trees),
+    endemic = TRUE,  # whether each clade is endemic
+    uncertain = FALSE  # whether colonization time is known for sure
+  )
+  metadata$endemic[3] <- FALSE
+  metadata$uncertain[2] <- TRUE
+ 
+  # Island age
+  age <- 5
+ 
+  # Make a plot
+  p <- DAISIE_plot_input(
+    trees,
+    age,
+    tcols,
+    metadata,
+    mapping = ggplot2::aes(color = endemic, linetype = uncertain),
+    pargs = list(size = 3)
+  )
+ p
+ }
Error in DataMask$new(.data, caller_env) : 
  argument "caller_env" is missing, with no default
Calls: DAISIE_plot_input ... mutate.data.frame -> mutate_cols -> <Anonymous> -> initialize
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.5Mb
Running 'testthat.R' [25s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dataspice)
  > 
  > test_check("dataspice")
  == Failed tests ================================================================
  -- Error (test-prep_access.R:38:3): prep_access works correctly ----------------
  Error: Cannot open file for writing:
  * 'D:\temp\RtmpCMS19N\data\metadata\access.csv'
  Backtrace:
      x
   1. \-dataspice::prep_access() test-prep_access.R:38:2
   2.   \-readr::write_csv(access, access_path)
   3.     \-readr::write_delim(...)
   4.       \-vroom::vroom_write(...)
   5.         \-vroom:::vroom_write_(...)
  -- Error (test-prep_attributes.R:60:1): (code run outside of `test_that()`) ----
  Error: Cannot open file for writing:
  * 'D:\temp\RtmpCMS19N\metadata\attributes.csv'
  Backtrace:
      x
   1. +-readr::read_csv(attributes_path)[0, ] %>% readr::write_csv(attributes_path) test-prep_attributes.R:60:0
   2. \-readr::write_csv(., attributes_path)
   3.   \-readr::write_delim(...)
   4.     \-vroom::vroom_write(...)
   5.       \-vroom:::vroom_write_(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 73 ]
  Error: Test failures
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.9Mb
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11009 (sockconn)
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

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

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

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11571 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11571 (sockconn)
Execution halted
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

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

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

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11769 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11769 (sockconn)
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   3.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/do.Rcheck/00install.out' for details.
Running examples in 'dowser-Ex.R' failed
The error most likely occurred in:

> ### Name: getTrees
> ### Title: Estimate lineage tree topologies, branch lengths, and internal
> ###   node states if desired
> ### Aliases: getTrees
> 
> ### ** Examples
> 
> data(ExampleClones)
> 
> trees <- getTrees(ExampleClones[10,])
> plotTrees(trees)[[1]]
Error in DataMask$new(.data, caller_env) : 
  argument "caller_env" is missing, with no default
Calls: plotTrees ... mutate.data.frame -> mutate_cols -> <Anonymous> -> initialize
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Building-Trees-Vignette.Rmd' using rmarkdown
Loading required package: ggplot2
--- finished re-building 'Building-Trees-Vignette.Rmd'

--- re-building 'Germlines-Vignette.Rmd' using rmarkdown
--- finished re-building 'Germlines-Vignette.Rmd'

--- re-building 'Plotting-Trees-Vignette.Rmd' using rmarkdown
Loading required package: ggplot2
Quitting from lines 40-53 (Plotting-Trees-Vignette.Rmd) 
Error: processing vignette 'Plotting-Trees-Vignette.Rmd' failed with diagnostics:
argument "caller_env" is missing, with no default
--- failed re-building 'Plotting-Trees-Vignette.Rmd'

--- re-building 'Quickstart-Vignette.Rmd' using rmarkdown
--- finished re-building 'Quickstart-Vignette.Rmd'

--- re-building 'Sequences-Vignette.Rmd' using rmarkdown
Loading required package: ggplot2
Quitting from lines 38-54 (Sequences-Vignette.Rmd) 
Error: processing vignette 'Sequences-Vignette.Rmd' failed with diagnostics:
argument "caller_env" is missing, with no default
--- failed re-building 'Sequences-Vignette.Rmd'

SUMMARY: processing the following files failed:
  'Plotting-Trees-Vignette.Rmd' 'Sequences-Vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'dub-vignette.Rmd' using rmarkdown
Loading required package: DUBStepR
Quitting from lines 50-53 (dub-vignette.Rmd) 
Error: processing vignette 'dub-vignette.Rmd' failed with diagnostics:
package or namespace load failed for 'Seurat' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace 'Matrix' 1.3-2 is already loaded, but >= 1.3.3 is required
--- failed re-building 'dub-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [65s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("dynutils")
  Loading required package: dynutils
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  == Failed tests ================================================================
  -- Failure (test-news.R:34:3): update_news works -------------------------------
  `find_news(path = dir_loc)` did not throw an error.
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 554 ]
  Error: Test failures
  Execution halted
Running 'testthat.R' [71s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("dynutils")
  Loading required package: dynutils
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  == Failed tests ================================================================
  -- Failure (test-news.R:34:3): update_news works -------------------------------
  `find_news(path = dir_loc)` did not throw an error.
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 554 ]
  Error: Test failures
  Execution halted
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Title: Trim and Format Address Information
> ### Aliases: trim_address
> 
> ### ** Examples
> 
> addr_string <- " 2 Dept of Urology, Feinberg School of Medicine," 
> addr_string <- paste(addr_string, "Chicago, US; Dept of Mol Bio as well...")
> print(addr_string)
[1] " 2 Dept of Urology, Feinberg School of Medicine, Chicago, US; Dept of Mol Bio as well..."
> print(trim_address(addr = addr_string))
[1] "Dept of Urology, Feinberg School of Medicine, Chicago, US"
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.92 0.89 488.32 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Running 'spelling.R' [0s]
  Running 'testthat.R' [37s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(evaluator)
  > 
  > # ensure phantom.js is available on CI platforms
  > if (Sys.getenv("NOT_CRAN", "") != "" || Sys.getenv("CI", "") != "") {
  +   if (!shinytest::dependenciesInstalled()) shinytest:::installDependencies()
  +   message("Using phantom.js from ", shinytest:::find_phantom(), "\n")
  + }
  > 
  > test_check("evaluator")
  # Scenario model: openfair_tef_tc_diff_lm
  == Skipped tests ===============================================================
  * Not running MVA test - EVALUATOR_TEST_MVA not set (1)
  * On CRAN (1)
  * Shiny testing is awkward, consider moving to stand along pkg (1)
  * empty test (1)
  
  == Failed tests ================================================================
  -- Error (test-reports.R:19:1): (code run outside of `test_that()`) ------------
  Error: Cannot open file for writing:
  * 'D:\temp\RtmpwfHoES\inputs\qualitative_scenarios.csv'
  Backtrace:
      x
   1. \-readr::write_csv(...) test-reports.R:19:0
   2.   \-readr::write_delim(...)
   3.     \-vroom::vroom_write(...)
   4.       \-vroom:::vroom_write_(...)
  
  [ FAIL 1 | WARN 1 | SKIP 4 | PASS 136 ]
  Error: Test failures
  Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(exampletestr)
  > 
  > get_os <- function() {
  +   sysinf <- Sys.info()
  +   if (!is.null(sysinf)) {
  +     os <- sysinf["sysname"]
  +     if (os == "Darwin") {
  +       os <- "osx"
  +     }
  +   } else { ## mystery machine
  +     os <- .Platform$OS.type
  +     if (grepl("^darwin", R.version$os)) {
  +       os <- "osx"
  +     }
  +     if (grepl("linux-gnu", R.version$os)) {
  +       os <- "linux"
  +     }
  +   }
  +   if (os == "osx") os <- "mac"
  +   tolower(os)
  + }
  > 
  > if (get_os() != "mac" || Sys.getenv("NOT_CRAN") == "true") {
  +   test_check("exampletestr")
  + }
  Error : [EBUSY] Failed to remove 'D:/temp/RtmpOm2gXf/tmpkg/tests/testthat/test-detect-examples--1.R': resource busy or locked
  == Failed tests ================================================================
  -- Error (test-files.R:65:3): `make_tests_shells_file()` and `make_tests_shells_pkg()` work --
  Error: Cannot open file for writing:
  * 'D:\temp\RtmpOm2gXf\tmpkg\tests\testthat\test-detect.R'
  Backtrace:
      x
   1. \-exampletestr::make_tests_shells_pkg(pkg_dir, overwrite = TRUE) test-files.R:65:2
   2.   +-withr::with_options(...)
   3.   | \-base::force(code)
   4.   \-purrr::map(...)
   5.     \-exampletestr:::.f(.x[[i]], ...)
   6.       \-readr::write_lines(combined, test_file_name)
   7.         \-vroom::vroom_write_lines(...)
   8.           \-vroom::vroom_write(...)
   9.             \-vroom:::vroom_write_(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 26 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  fgsg.h:96:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:202:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:347:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:460:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:516:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:636:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:717:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:852:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:996:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0/FGSG.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'intro_to_fishflux.Rmd' using rmarkdown
Executing: pandoc -t html -o "D:\temp\Rtmpsb32km\file1b79c139a77f5.html" "D:\temp\Rtmpsb32km\file1b79c139a77f5.tex"
Quitting from lines 131-133 (intro_to_fishflux.Rmd) 
Error: processing vignette 'intro_to_fishflux.Rmd' failed with diagnostics:

GitHub API error (401): 
Message: Bad credentials
Read more at https://docs.github.com/rest
--- failed re-building 'intro_to_fishflux.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
installed size is 107.7Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    doc      1.0Mb
    gdal     2.1Mb
    libs    92.8Mb
    proj     8.7Mb
Running examples in 'genBaRcode-Ex.R' failed
The error most likely occurred in:

> ### Name: plotClusterGgTree
> ### Title: Plotting a Cluster ggTree
> ### Aliases: plotClusterGgTree
> 
> ### ** Examples
> 
> data(BC_dat)
> plotClusterGgTree(BC_dat, tree_est = "UPGMA", type = "circular")
Error in DataMask$new(.data, caller_env) : 
  argument "caller_env" is missing, with no default
Calls: plotClusterGgTree ... mutate.data.frame -> mutate_cols -> <Anonymous> -> initialize
Execution halted
Error(s) in re-building vignettes:
--- re-building 'genBaRcode_GUI_Vignette.Rmd' using rmarkdown
--- finished re-building 'genBaRcode_GUI_Vignette.Rmd'

--- re-building 'genBaRcode_Vignette.Rmd' using rmarkdown
Quitting from lines 692-696 (genBaRcode_Vignette.Rmd) 
Error: processing vignette 'genBaRcode_Vignette.Rmd' failed with diagnostics:
argument "caller_env" is missing, with no default
--- failed re-building 'genBaRcode_Vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ###   Decimal degrees.
> ### Aliases: sexagesimal
> 
> ### ** Examples
> 
> # Latitude
> g <- -33
> m <- 38
> s <- 30.123456
> value <- sexagesimal(g, m, s, digits = 4)
> print(value)
[1] -33.6417
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  12.11 0.66 12.99 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
make_gradient_fill: no visible binding for global variable
  'linearGradient'
Undefined global functions or variables:
  linearGradient
create_gradient_as_geometry: no visible global function definition for
  'linearGradient'
create_gradient_as_geometry: no visible global function definition for
  'radialGradient'
Undefined global functions or variables:
  linearGradient radialGradient
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hazer)
  > 
  > test_check("hazer")
  == Failed tests ================================================================
  -- Failure (testall.R:22:3): test the haze -------------------------------------
  floor(h$haze * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 225, 224).
  1/1 mismatches
  [1] 224 - 225 == -1
  -- Failure (testall.R:23:3): test the haze -------------------------------------
  floor(h$A0 * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 710, 712).
  1/1 mismatches
  [1] 712 - 710 == 2
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11510 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11510 (sockconn)
Execution halted
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11480 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11480 (sockconn)
Execution halted
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/4.0/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  d:/RCompile/CRANpkg/lib/4.0/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  d:/RCompile/CRANpkg/lib/4.0/BH/include/boost/container/detail/copy_move_algo.hpp:909:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.0/lolog.Rcheck/00install.out' for details.
Found the following significant warnings:
  lxb.c:62:21: warning: '%d' directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0/lxb.Rcheck/00install.out' for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Running examples in 'migest-Ex.R' failed
The error most likely occurred in:

> ### Name: index_distance
> ### Title: Summary indices of migration distance
> ### Aliases: index_distance
> 
> ### ** Examples
> 
> # single year
> index_distance(
+   m = subset(korea_reg, year == 2020), 
+   d = korea_dist
+ )
Error in index_distance(m = subset(korea_reg, year == 2020), d = korea_dist) : 
  different region names in m and d
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mlpack.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mpmi.Rcheck/00install.out' for details.
Running 'test-all.R' [65s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > 
  > library(testthat)
  > 
  > test_check("mudata2")
  Loading required package: mudata2
  
  Attaching package: 'mudata2'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  == Skipped tests ===============================================================
  * On CRAN (2)
  
  == Failed tests ================================================================
  -- Error (test-mudata-io.R:114:3): type strs are guessed when inappropriate columns exist in columns tbl --
  Error: Error writing mudata to CSV:
   _mudata.csv: Error : Cannot open file for writing:
  * 'D:\temp\RtmpGaz9NJ\file6e2c7f593680\_mudata.csv'
  
  Backtrace:
      x
   1. \-mudata2::write_mudata_dir(...) test-mudata-io.R:114:2
  
  [ FAIL 1 | WARN 1 | SKIP 2 | PASS 891 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0/NestedCategBayesImpute.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'Introducing_nhanesA.Rmd' using rmarkdown
Quitting from lines 159-163 (Introducing_nhanesA.Rmd) 
Error: processing vignette 'Introducing_nhanesA.Rmd' failed with diagnostics:
OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 10054
--- failed re-building 'Introducing_nhanesA.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    CppCode   2.7Mb
    R         5.8Mb
    include   5.8Mb
    libs      2.4Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/OpenCL.Rcheck/00install.out' for details.
Running 'exporting-methods.R' [3s]
  Running 'testthat.R' [32s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  == Failed tests ================================================================
  -- Error (test.match_on.R:591:5): standardization_scale with svyglm ------------
  Error: non-numeric argument to binary operator
  Backtrace:
      x
   1. \-optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   \-optmatch:::standardizer(des_t)
   3.     +-stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     \-survey:::update.survey.design(...)
   5.       \-base::eval(dots[[j]], object$variables, parent.frame())
   6.         \-base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1603 ]
  Error: Test failures
  Execution halted
Running 'exporting-methods.R' [3s]
  Running 'testthat.R' [34s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  == Failed tests ================================================================
  -- Error (test.match_on.R:591:5): standardization_scale with svyglm ------------
  Error: non-numeric argument to binary operator
  Backtrace:
      x
   1. \-optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   \-optmatch:::standardizer(des_t)
   3.     +-stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     \-survey:::update.survey.design(...)
   5.       \-base::eval(dots[[j]], object$variables, parent.frame())
   6.         \-base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1603 ]
  Error: Test failures
  Execution halted
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    doc    9.3Mb
    libs   6.3Mb
Found the following significant warnings:
  putty/windows/winstore.c:665:38: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
  putty/windows/winstore.c:673:42: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0/pbdRPC.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'PCMBase.Rmd' using rmarkdown
Quitting from lines 272-302 (PCMBase.Rmd) 
Error: processing vignette 'PCMBase.Rmd' failed with diagnostics:
argument "caller_env" is missing, with no default
--- failed re-building 'PCMBase.Rmd'

--- re-building 'PCMCreateModel.Rmd' using rmarkdown
Quitting from lines 356-386 (PCMCreateModel.Rmd) 
Error: processing vignette 'PCMCreateModel.Rmd' failed with diagnostics:
argument "caller_env" is missing, with no default
--- failed re-building 'PCMCreateModel.Rmd'

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

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

SUMMARY: processing the following files failed:
  'PCMBase.Rmd' 'PCMCreateModel.Rmd'

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

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11884 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11884 (sockconn)
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
    libs      2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/PhitestR.Rcheck/00install.out' for details.
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ratelimitr)
  > 
  > test_check("ratelimitr")
  == Skipped tests ===============================================================
  * On CRAN (1)
  
  == Failed tests ================================================================
  -- Failure (test-function-errors.R:22:5): rate limits still work in face of errors --
  min(times, na.rm = TRUE) is not strictly more than `period`. Difference: -0.0086
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 18 ]
  Error: Test failures
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0/Rblpapi.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rcplex.Rcheck/00install.out' for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      2.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      2.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    lib       4.6Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rcrypt.Rcheck/00install.out' for details.
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0/RDieHarder.Rcheck/00install.out' for details.
installed size is 107.4Mb
  sub-directories of 1Mb or more:
    doc        3.4Mb
    gdal       2.2Mb
    libs      89.4Mb
    pictures   1.3Mb
    proj       8.7Mb
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
ggtree v2.4.2  For help: https://yulab-smu.top/treedata-book/

If you use ggtree in published research, please cite the most appropriate paper(s):

1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96
2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
3. Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628


Loading required package: ape

Attaching package: 'ape'

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

    rotate

Loading required package: maps
Warning in load_fasta(fasta.file.name) :
  Characters not in acgtnACGTN- will be treated as missing (-)...
Warning in load_fasta(woodmouse) :
  Characters not in acgtnACGTN- will be treated as missing (-)...
Read 1 item
Quitting from lines 106-110 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
argument "caller_env" is missing, with no default
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  fakemaster.c:82:57: warning: embedded '\0' in format [-Wformat-contains-nul]
See 'd:/Rcompile/CRANpkg/local/4.0/Rhpc.Rcheck/00install.out' for details.
Found the following significant warnings:
  RInside.cpp:169:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 260 equals destination size [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0/RInside.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/4.0/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.9Mb
Loading this package had a fatal error status code 1
Loading log:
Loading required package: Matrix
Error: package or namespace load failed for 'Rmagic':
 .onLoad failed in loadNamespace() for 'Rmagic', details:
  call: NULL
  error: lexical error: invalid char in json text.
                                       NA
                     (right here) ------^
Execution halted
Found the following significant warnings:
  RlibMVL.c:771:9: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0/RMVL.Rcheck/00install.out' for details.
Running 'someFIGIs.R' [12s]
Running the tests in 'tests/someFIGIs.R' failed.
Complete output:
  > library(ROpenFIGI)
  > jsondf <- data.frame(idType=c("ID_ISIN"),idValue=c("US922646AS37"),
  +                      exchCode=c(NA),currency=NA,micCode=NA,stringsAsFactors = F)
  > 
  > jsonrst <- OpenFIGI(jsondf)
  Error in curl::curl_fetch_memory(url, handle = handle) : 
    Timeout was reached: [api.openfigi.com] Resolving timed out after 10000 milliseconds
  Calls: OpenFIGI ... request_fetch -> request_fetch.write_memory -> <Anonymous>
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ROracle.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rPanglaoDB.Rcheck/00install.out' for details.
Found the following significant warnings:
  cli.c:232:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0/RSclient.Rcheck/00install.out' for details.
Found the following significant warnings:
  RSserver.c:64:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/4.0/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6607 and 7237 may overlap 1 byte at offset 7237 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6607 and 7237 may overlap 1 byte at offset 7237 [-Wrestrict]
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0/RSNNS.Rcheck/00install.out' for details.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Name: SolrList-class
> ### Title: SolrList
> ### Aliases: class:SolrList SolrList-class length,SolrList-method
> ###   names,SolrList-method [<-,SolrList,ANY,ANY,ANY-method
> ###   [[,SolrList,ANY-method [,SolrList-method [[,SolrList-method
> ###   [[<-,SolrList-method unique,SolrList-method searchDocs
> ###   searchDocs,Solr SolrList coerce,Solr,SolrList-method
> ###   coerce,SolrList,DocCollection-method show,SolrList-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.5 0.11 3.6 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R version 4.0.0 RC (2020-04-17 r78247)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6003) Service Pack 2

Matrix products: default

locale:
[1] LC_COLLATE=C                 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=C                LC_NUMERIC=C                
[5] LC_TIME=C                   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_4.0.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
Error(s) in re-building vignettes:
--- re-building 'quickstart.Rmd' using rmarkdown
Loading required package: raster
Loading required package: sp
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 3.2.1, released 2020/12/29
Path to GDAL shared files: D:/temp/RtmpQF0kW6/RLIBS_8c2c933722b/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: D:/temp/RtmpQF0kW6/RLIBS_8c2c933722b/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 D:/temp/RtmpQF0kW6/RLIBS_8c2c933722b/rgdal/proj
Warning in utils::download.file(url, tmp, quiet = TRUE) :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
trying URL 'http://www.lifewatch.be/sdmpredictors/BO_ph_lonlat.tif'
Quitting from lines 79-91 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
cannot open URL 'http://www.lifewatch.be/sdmpredictors/BO_ph_lonlat.tif'
--- failed re-building 'quickstart.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Seurat.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Signac.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'SimPhe.Rmd' using rmarkdown
Quitting from lines 157-167 (SimPhe.Rmd) 
Error: processing vignette 'SimPhe.Rmd' failed with diagnostics:
'data' must be of a vector type, was 'NULL'
--- failed re-building 'SimPhe.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/4.0/SongEvo.Rcheck/
vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20population\%2
0size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.0/SongEvo.Rcheck/vign_test/SongEvo/vignettes/SongEvo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SongEvo.log for more info.
--- failed re-building 'SongEvo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SoupX.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.3Mb
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.5)
than is installed on your system (1.0.6). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.5)
than is installed on your system (1.0.6). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.5)
than is installed on your system (1.0.6). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    include  10.1Mb
Running examples in 'STraTUS-Ex.R' failed
The error most likely occurred in:

> ### Name: build.edgelist
> ### Title: For a sample, produce the transmission tree as a 'igraph' object
> ### Aliases: build.edgelist
> 
> ### ** Examples
> 
> generator <- tt.generator(stratus.example.tree)
> samples <- sample.tt(generator, 1)
Error in DataMask$new(.data, caller_env) : 
  argument "caller_env" is missing, with no default
Calls: sample.tt ... mutate.data.frame -> mutate_cols -> <Anonymous> -> initialize
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.4Mb
    libs   2.2Mb
Error(s) in re-building vignettes:
--- re-building 'HierarchicalModels.Rmd' using knitr
Quitting from lines 27-29 (HierarchicalModels.Rmd) 
Error: processing vignette 'HierarchicalModels.Rmd' failed with diagnostics:
Could not find feasible matrix. Subrectangle in row(s) 5 and column(s) 5 violates existence condition.
--- failed re-building 'HierarchicalModels.Rmd'

--- re-building 'Introduction.Rmd' using knitr
--- finished re-building 'Introduction.Rmd'

--- re-building 'NonSquare.Rmd' using knitr
--- finished re-building 'NonSquare.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 108.4Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    gdal   2.1Mb
    libs  94.1Mb
    proj   8.7Mb
Running 'testthat.R' [26s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > test_check("tibble")
  Loading required package: tibble
  Starting 2 test processes
  == Skipped tests ===============================================================
  * All of them (1)
  * Do we want an .as_row argument? (1)
  * Installed rlang is version 0.4.11; but 0.4.11.9001 is required (1)
  * Non-UTF-8 locale (7)
  * On CRAN (32)
  * On Windows (1)
  * packageVersion("tibble") >= "2.99.99" is TRUE (93)
  
  == Failed tests ================================================================
  -- Failure (test-zzz-trunc-mat.R:15:3): interface of print() identical to trunc_mat() --
  `print_arg_names_without` (`actual`) not equal to `trunc_mat_arg_names_without` (`expected`).
  
  `actual`:   "x" "n" "max_extra_cols" "max_footer_lines"
  `expected`: "x" "n" "n_extra"                          
  
  [ FAIL 1 | WARN 0 | SKIP 136 | PASS 1314 ]
  Error: Test failures
  Execution halted
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > test_check("tibble")
  Loading required package: tibble
  Starting 2 test processes
  == Skipped tests ===============================================================
  * All of them (1)
  * Do we want an .as_row argument? (1)
  * Installed rlang is version 0.4.11; but 0.4.11.9001 is required (1)
  * Non-UTF-8 locale (7)
  * On CRAN (32)
  * On Windows (1)
  * packageVersion("tibble") >= "2.99.99" is TRUE (93)
  
  == Failed tests ================================================================
  -- Failure (test-zzz-trunc-mat.R:15:3): interface of print() identical to trunc_mat() --
  `print_arg_names_without` (`actual`) not equal to `trunc_mat_arg_names_without` (`expected`).
  
  `actual`:   "x" "n" "max_extra_cols" "max_footer_lines"
  `expected`: "x" "n" "n_extra"                          
  
  [ FAIL 1 | WARN 0 | SKIP 136 | PASS 1314 ]
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/tidyseurat.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'structuredCoalescent.Rmd' using rmarkdown
Quitting from lines 64-65 (structuredCoalescent.Rmd) 
Error: processing vignette 'structuredCoalescent.Rmd' failed with diagnostics:
argument "caller_env" is missing, with no default
--- failed re-building 'structuredCoalescent.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/vctrs.Rcheck/00install.out' for details.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0/x13binary.Rcheck/00install.out' for details.
Running examples in 'xpose4-Ex.R' failed
The error most likely occurred in:

> ### Name: simprazExample
> ### Title: Function to create files for the simulated prazosin example in
> ###   Xpose
> ### Aliases: simprazExample
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> od = setwd(tempdir()) # move to a temp directory
> (cur.files <- dir()) # current files in temp directory
[1] "pdfcf6c7d487f05" "xptab1"         
> 
> simprazExample(overwrite=TRUE) # write files
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'xptab1': Invalid argument
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: simprazExample -> writeTab -> cat -> file
Execution halted
Error(s) in re-building vignettes:
--- re-building 'gammaproteobacteria.Rmd' using rmarkdown
ggtree v2.4.2  For help: https://yulab-smu.top/treedata-book/

If you use ggtree in published research, please cite the most appropriate paper(s):

1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96
2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
3. Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628



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 80-83 (gammaproteobacteria.Rmd) 
Error: processing vignette 'gammaproteobacteria.Rmd' failed with diagnostics:
argument "caller_env" is missing, with no default
--- failed re-building 'gammaproteobacteria.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'geographic.Rmd' using knitr
--- finished re-building 'geographic.Rmd'

--- re-building 'zipcodeR.Rmd' using knitr
Quitting from lines 15-20 (zipcodeR.Rmd) 
Error: processing vignette 'zipcodeR.Rmd' failed with diagnostics:
Timeout was reached: [econdata.s3-us-west-2.amazonaws.com] Resolving timed out after 10000 milliseconds
--- failed re-building 'zipcodeR.Rmd'

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

Error: Vignette re-building failed.
Execution halted