installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.0Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/bigtabulate.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BinQuasi.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Biograph.Rcheck/00install.out' for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/biomartr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BioMedR.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.3Mb
    extdata   1.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.5Mb
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in 'biscale-Ex.R' failed
The error most likely occurred in:

> ### Name: bi_class
> ### Title: Create Classes for Bivariate Maps
> ### Aliases: bi_class
> 
> ### ** Examples
> 
> # quantile breaks, 2x2
> data <- bi_class(stl_race_income, x = pctWhite, y = medInc, style = "quantile", dim = 2)
Warning in bi_class(stl_race_income, x = pctWhite, y = medInc, style = "quantile",  :
  The 'sf' package is not loaded, and the class 'sf' attribute of the given data set has been lost. Load 'sf' to retain the class when using 'bi_class'.
Error: All columns in a tibble must be vectors.
x Column `geometry` is a `sfc_POLYGON/sfc` object.
Backtrace:
     x
  1. \-biscale::bi_class(...)
  2.   +-dplyr::mutate(.data, bi_x = cut(!!xQ, breaks = bins_x, include.lowest = TRUE))
  3.   \-dplyr:::mutate.data.frame(...)
  4.     +-base::as.data.frame(mutate(tbl_df(.data), ...))
  5.     +-dplyr::mutate(tbl_df(.data), ...)
  6.     \-dplyr::tbl_df(.data)
  7.       +-tibble::as_tibble(data, .name_repair = "check_unique")
  8.       \-tibble:::as_tibble.data.frame(data, .name_repair = "check_unique")
  9.         \-tibble:::lst_to_tibble(unclass(x), .rows, .name_repair)
 10.           \-tibble:::check_valid_cols(x)
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(biscale)
  > 
  > test_check("biscale")
  -- 1. Error: sf warning is triggered (@test_bi_class.R#10)  --------------------
  All columns in a tibble must be vectors.
  x Column `geometry` is a `sfc_POLYGON/sfc` object.
  Backtrace:
    1. testthat::expect_warning(...)
    6. biscale::bi_class(...)
    8. dplyr:::mutate.data.frame(...)
   11. dplyr::tbl_df(.data)
   13. tibble:::as_tibble.data.frame(data, .name_repair = "check_unique")
   14. tibble:::lst_to_tibble(unclass(x), .rows, .name_repair)
   15. tibble:::check_valid_cols(x)
  
  == testthat results  ===========================================================
  [ OK: 82 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: sf warning is triggered (@test_bi_class.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BiSEp.Rcheck/00install.out' for details.
Running examples in 'blandr-Ex.R' failed
The error most likely occurred in:

> ### Name: blandr.dataset.fibre
> ### Title: Function to load D'arbela mean velocity of circumferential fibre
> ###   shortening dataset from internet
> ### Aliases: blandr.dataset.fibre
> 
> ### ** Examples
> 
> blandr.dataset.fibre()
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: blandr.dataset.fibre -> readLines -> file
Execution halted
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running examples in 'blscrapeR-Ex.R' failed
The error most likely occurred in:

> ### Name: inflation_adjust
> ### Title: Convert the Value of a US Dollar to a Given Year
> ### Aliases: inflation_adjust
> ### Keywords: api bls cpi economics inflation unemployment
> 
> ### ** Examples
> 
> 
> ## Get historical USD values based on a 2010 dollar.
> values <- inflation_adjust(base_year = 2015)
trying URL 'https://download.bls.gov/pub/time.series/cu/cu.data.1.AllItems'
Warning in download.file("https://download.bls.gov/pub/time.series/cu/cu.data.1.AllItems",  :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in download.file("https://download.bls.gov/pub/time.series/cu/cu.data.1.AllItems",  : 
  cannot open URL 'https://download.bls.gov/pub/time.series/cu/cu.data.1.AllItems'
Calls: inflation_adjust -> download.file
Execution halted
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BMTME)
  > 
  > test_check("BMTME")
  -- 1. Failure: RandomPartition (@test.R#52)  -----------------------------------
  RP_Test$Environments inherits from `character` not `factor`.
  
  -- 2. Failure: RandomPartition (@test.R#72)  -----------------------------------
  RP_Test2$Traits inherits from `character` not `factor`.
  
  == testthat results  ===========================================================
  [ OK: 164 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: RandomPartition (@test.R#52) 
  2. Failure: RandomPartition (@test.R#72) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [29s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BMTME)
  > 
  > test_check("BMTME")
  -- 1. Failure: RandomPartition (@test.R#52)  -----------------------------------
  RP_Test$Environments inherits from `character` not `factor`.
  
  -- 2. Failure: RandomPartition (@test.R#72)  -----------------------------------
  RP_Test2$Traits inherits from `character` not `factor`.
  
  == testthat results  ===========================================================
  [ OK: 164 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: RandomPartition (@test.R#52) 
  2. Failure: RandomPartition (@test.R#72) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BonEV.Rcheck/00install.out' for details.
installed size is 59.5Mb
  sub-directories of 1Mb or more:
    include   8.5Mb
    lib      50.6Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running examples in 'brazilmaps-Ex.R' failed
The error most likely occurred in:

> ### Name: get_brmap
> ### Title: Get Brazilian maps from different geographic levels
> ### Aliases: get_brmap
> ### Keywords: IBGE geographic levels shapefile spatial
> 
> ### ** Examples
> 
> ## Retrieving the map from the State of Rio de Janeiro
> rio_map <- get_brmap(geo = "State",
+                      geo.filter = list(State = 33),
+                      class = "sf")
Error: All columns in a tibble must be vectors.
x Column `geometry` is a `sfc_MULTIPOLYGON/sfc` object.
Backtrace:
     x
  1. \-brazilmaps::get_brmap(...)
  2.   \-`%>%`(...)
  3.     +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4.     \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.         \-brazilmaps:::`_fseq`(`_lhs`)
  7.           \-magrittr::freduce(value, `_function_list`)
  8.             \-function_list[[i]](value)
  9.               +-dplyr::filter(., brmap[[(names(geo.filter)[i])]] %in% geo.filter[[i]])
 10.               \-dplyr:::filter.data.frame(...)
 11.                 +-base::as.data.frame(filter(tbl_df(.data), ..., .preserve = .preserve))
 12.                 +-dplyr::filter(tbl_df(.data), ..., .preserve = .preserve)
 13.                 \-dplyr::tbl_df(.data)
 14.                   +-tibble::as_tibble(data, .name_repair = "check_unique")
 15.                   \-tibble:::as_tibble.data.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     3.5Mb
    doc   2.6Mb
Error(s) in re-building vignettes:
--- re-building 'broom_mixed_intro.rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.

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

Registered S3 methods overwritten by 'broom.mixed':
  method         from 
  augment.lme    broom
  augment.merMod broom
  glance.lme     broom
  glance.merMod  broom
  glance.stanreg broom
  tidy.brmsfit   broom
  tidy.gamlss    broom
  tidy.lme       broom
  tidy.merMod    broom
  tidy.rjags     broom
  tidy.stanfit   broom
  tidy.stanreg   broom
Loading required package: brms
Loading required package: Rcpp
Loading 'brms' package (version 2.12.0). Useful instructions
can be found by typing help('brms'). A more detailed introduction
to the package is available through vignette('brms_overview').

Attaching package: 'brms'

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

    ar

Loading required package: dotwhisker
Loading required package: ggplot2
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 68-82 (broom_mixed_intro.rmd) 
Error: processing vignette 'broom_mixed_intro.rmd' failed with diagnostics:
Aesthetics must be either length 1 or the same as the data (6): xmin and xmax
--- failed re-building 'broom_mixed_intro.rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'brt.rmd' using rmarkdown
Quitting from lines 147-156 (brt.rmd) 
Error: processing vignette 'brt.rmd' failed with diagnostics:
package 'S4Vectors' could not be loaded
--- failed re-building 'brt.rmd'

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

Error: Vignette re-building failed.
Execution halted
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Brundle.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.0Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/cate.Rcheck/00install.out' for details.
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/ceg.Rcheck/00install.out' for details.
Warning: multiple methods tables found for 'plot'

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.
Running examples in 'ceg-Ex.R' failed
The error most likely occurred in:

> ### Name: plot,Stratified.ceg.model,ANY-method
> ### Title: Stratified.ceg.model Plotting
> ### Aliases: plot,Stratified.ceg.model,ANY-method
> 
> ### ** Examples
> 
> plot(scm)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CensMFM.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/CePa.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
--- finished re-building 'Introduction.Rmd'

--- re-building 'Visualising_Interactions.Rmd' using rmarkdown
Loading required package: InteractionSet
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

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

Loading required package: S4Vectors
Error: package or namespace load failed for 'S4Vectors':
 .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Quitting from lines 41-105 (Visualising_Interactions.Rmd) 
Error: processing vignette 'Visualising_Interactions.Rmd' failed with diagnostics:
package 'S4Vectors' could not be loaded
--- failed re-building 'Visualising_Interactions.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
  Warning: found methods to import for function 'plot' but not the generic itself
See 'd:/Rcompile/CRANpkg/local/4.0/classGraph.Rcheck/00install.out' for details.
Warning: found methods to import for function 'plot' but not the generic itself

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.
Running examples in 'classGraph-Ex.R' failed
The error most likely occurred in:

> ### Name: bGraph
> ### Title: Create a "Branch Graph" (Simple Tree with Root and Leaves)
> ### Aliases: bGraph
> ### Keywords: graphs
> 
> ### ** Examples
> 
> require("graph") ## Using package 'graph' => plot() method (via package 'Rgraphviz'):
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

> 
> (bg7 <- bGraph(7)) # 8 nodes {Mom, D1..D7}; 7 edges
A graphNEL graph with undirected edges
Number of Nodes = 8 
Number of Edges = 7 
> plot(bg7) # draws the graph
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot -> plot -> plot.default -> xy.coords
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CleanBSequences.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Running 'testthat.R' [180s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clubSandwich)
  Registered S3 method overwritten by 'clubSandwich':
    method    from    
    bread.mlm sandwich
  > 
  > test_check("clubSandwich")
  -- 1. Failure: Order doesn't matter. (@test_lmerMod.R#153)  --------------------
  `Wald_fit` not equal to `Wald_scramble`.
  Component 19: Component 4: Mean relative difference: 1.550446e-08
  
  == testthat results  ===========================================================
  [ OK: 754 | SKIPPED: 11 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Order doesn't matter. (@test_lmerMod.R#153) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/clustermole.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:

======== End of example output (where/before crash/hang up occured ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CNVScope.Rcheck/00install.out' for details.
Running examples in 'CodeDepends-Ex.R' failed
The error most likely occurred in:

> ### Name: makeCallGraph
> ### Title: Create a graph representing which functions call other functions
> ### Aliases: makeCallGraph makeCallGraph,list-method
> ###   makeCallGraph,character-method makeCallGraph,function-method
> ### Keywords: hplot programming
> 
> ### ** Examples
> 
> 
>   gg = makeCallGraph("package:CodeDepends")
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

>   if(require(Rgraphviz)) {
+      plot(gg, "twopi")
+ 
+      ag = agopen(gg, layoutType = "circo", name = "bob")
+      plot(ag)
+   }
Loading required package: Rgraphviz
Loading required package: grid
Warning: multiple methods tables found for 'plot'
Error in as.double(x) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot ... eval -> eval -> .nextMethod -> plot.default -> xy.coords
Execution halted
Running 'draw.R' [2s]
  Running 'inputs.R' [2s]
  Running 'thread.R' [3s]
  Running 'varDeps.R' [2s]
Running the tests in 'tests/draw.R' failed.
Complete output:
  > library(CodeDepends)
  > library(Rgraphviz)
  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
  
  Loading required package: grid
  Warning message:
  multiple methods tables found for 'plot' 
  > sc = readScript(system.file("samples", "parallel.R", package = "CodeDepends"))
  > 
  > g = makeVariableGraph(,sc)
  > plot(g)
  Error in as.double(y) : 
    cannot coerce type 'S4' to vector of type 'double'
  Calls: plot -> plot -> plot.default -> xy.coords
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'intro.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 144-150 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'intro.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/cogmapr.Rcheck/00install.out' for details.
Running examples in 'cogmapr-Ex.R' failed
The error most likely occurred in:

> ### Name: plotIndCMap
> ### Title: Plotting an Individual Cognitive Map
> ### Aliases: plotIndCMap
> 
> ### ** Examples
> 
> project_name <- "a_new_project"
> main_path <- paste0(system.file("testdata", package = "cogmapr"), '/')
> my.project <- ProjectCMap(main_path, project_name)
> 
> icm <- IndCMap(my.project, 1)
> 
> plotIndCMap(icm)
Error in as.double(x) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plotIndCMap ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.8Mb
Error(s) in re-building vignettes:
--- re-building 'collateral.Rmd' using rmarkdown
Quitting from lines 221-229 (collateral.Rmd) 
Error: processing vignette 'collateral.Rmd' failed with diagnostics:
Input must be a vector, not a `safely_mapped` object.
--- failed re-building 'collateral.Rmd'

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

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

> ### Name: scale_colour_continuous_diverging
> ### Title: HCL-Based Continuous Diverging Color Scales for ggplot2
> ### Aliases: scale_colour_continuous_diverging
> ###   scale_color_continuous_diverging scale_fill_continuous_diverging
> 
> ### ** Examples
> 
> # adapted from stackoverflow: https://stackoverflow.com/a/20127706/4975218
> 
> library("ggplot2")
> 
> # generate dataset and base plot
> set.seed(100)
> df <- data.frame(country = LETTERS, V = runif(26, -40, 40))
> df$country = factor(LETTERS, LETTERS[order(df$V)]) # reorder factors
> gg <- ggplot(df, aes(x = country, y = V, fill = V)) +
+   geom_bar(stat = "identity") +
+   labs(y = "Under/over valuation in %", x = "Country") +
+   coord_flip() + theme_minimal()
>   
> # plot with default diverging scale
> gg + scale_fill_continuous_diverging()
Error in if (!alpha || all(lab_in[, 4] == 1)) { : 
  missing value where TRUE/FALSE needed
Calls: scale_fill_continuous_diverging ... <Anonymous> -> ggproto -> <Anonymous> -> colour_ramp
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   2.0Mb
Running examples in 'concaveman-Ex.R' failed
The error most likely occurred in:

> ### Name: concaveman
> ### Title: concaveman: A very fast 2D concave hull algorithm.
> ### Aliases: concaveman concaveman-package concaveman concaveman.matrix
> ###   concaveman.sf concaveman.SpatialPoints
> 
> ### ** Examples
> 
> data(points)
> polygons <- concaveman(points)
Error: All columns in a tibble must be vectors.
x Column `geometry` is a `sfc_POINT/sfc` object.
Backtrace:
     x
  1. +-concaveman::concaveman(points)
  2. \-concaveman:::concaveman.sf(points)
  3.   \-`%>%`(...)
  4.     +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  5.     \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.       \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
  7.         \-concaveman:::`_fseq`(`_lhs`)
  8.           \-magrittr::freduce(value, `_function_list`)
  9.             +-base::withVisible(function_list[[k]](value))
 10.             \-function_list[[k]](value)
 11.               +-dplyr::summarise(...)
 12.               \-dplyr:::summarise.data.frame(...)
 13.                 +-base::as.data.frame(summarise(tbl_df(.data), ...))
 14.                 +-dplyr::summarise(tbl_df(.data), ...)
 15.                 \-dplyr::tbl_df(.data)
 16.                   +-tibble::as_tibble(data, .name_repair = "check_unique")
 17.                   \-tibble:
Execution halted
Running examples in 'concurve-Ex.R' failed
The error most likely occurred in:

> ### Name: curve_corr
> ### Title: Computes Consonance Intervals for Correlations
> ### Aliases: curve_corr
> 
> ### ** Examples
> 
> 
> GroupA <- rnorm(50)
> GroupB <- rnorm(50)
> joe <- curve_corr(x = GroupA, y = GroupB, alternative = "two.sided", method = "pearson")
> tibble::tibble(joe[[1]])
Error: All columns in a tibble must be vectors.
x Column `joe[[1]]` is a `data.frame/concurve` object.
Backtrace:
    x
 1. \-tibble::tibble(joe[[1]])
 2.   \-tibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
 3.     \-tibble:::check_valid_col(res, col_names[[j]], j)
 4.       \-tibble:::check_valid_cols(set_names(list(x), name))
Execution halted
Error(s) in re-building vignettes:
--- re-building 'examples.Rmd' using rmarkdown
Quitting from lines 51-52 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
All columns in a tibble must be vectors.
x Column `intervalsdf[[1]]` is a `data.frame/concurve` object.
--- failed re-building 'examples.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CONDOP.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Running examples in 'convergEU-Ex.R' failed
The error most likely occurred in:

> ### Name: country_ranking
> ### Title: Ranking of EU countries by time
> ### Aliases: country_ranking
> 
> ### ** Examples
> 
> 
> # Example 1
> # Sorted dataframe in the format years by countries:
> require(tibble)
Loading required package: tibble
> myTB  <- tibble::tribble(
+ ~years, ~UK, ~DE, ~IT,
+ 1988,   1201, 868, 578,
+ 1989,   1150, 978, 682,
+ 1990,   998,  1250, 332,
+ 1991,  1600,  1350, 802
+ )
> 
> # Country ranking according to the indicator higher is the best:
> res <- country_ranking(myTB,timeName="years")
Error: Assigned data `rank(unlist(ord_MS[auxMS, -posizTime]), ties.method = "min")` must be compatible with row subscript `auxMS`.
x 1 row must be assigned.
x Assigned data has 3 rows.
i Only vectors of size 1 are recycled.
Backtrace:
    x
 1. \-convergEU::country_ranking(myTB, timeName = "years")
 2.   +-base::`[<-`(...)
 3.   \-tibble:::`[<-.tbl_df`(...)
 4.     \-tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       \-tibble:::vectbl_recycle_rhs(...)
 6.         \-base::tryCatch(...)
 7.           \-base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               \-value[[3L]](cond)
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
Running examples in 'corpus-Ex.R' failed
The error most likely occurred in:

> ### Name: text_locate
> ### Title: Searching for Terms
> ### Aliases: text_count text_detect text_locate text_match text_sample
> ###   text_subset
> 
> ### ** Examples
> 
> text <- c("Rose is a rose is a rose is a rose.",
+           "A rose by any other name would smell as sweet.",
+           "Snow White and Rose Red")
> 
> text_count(text, "rose")
[1] 4 1 1
> text_detect(text, "rose")
[1] TRUE TRUE TRUE
> text_locate(text, "rose")
Error in sum(colwidths) : invalid 'type' (list) of argument
Calls: <Anonymous> ... print.corpus_text_locate -> format.corpus_text_locate
Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  == testthat results  ===========================================================
  [ OK: 594 | SKIPPED: 8 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  == testthat results  ===========================================================
  [ OK: 594 | SKIPPED: 8 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    libs      1.5Mb
Package suggested but not available for checking: 'ProData'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
Running examples in 'countToFPKM-Ex.R' failed
The error most likely occurred in:

> ### Name: fpkmheatmap
> ### Title: Convert Counts to Fragments per Kilobase of Transcript per
> ###   Million (FPKM) A FPKM heatmap plot of the highly variable features in
> ###   RNA-Seq dataset
> ### Aliases: fpkmheatmap
> 
> ### ** Examples
> 
> library(countToFPKM)
> 
> file.readcounts <- system.file("extdata", "RNA-seq.read.counts.csv", package="countToFPKM")
> file.annotations <- system.file("extdata", "Biomart.annotations.hg38.txt", package="countToFPKM")
> file.sample.metrics <- system.file("extdata", "RNA-seq.samples.metrics.txt", package="countToFPKM")
> 
> 
> # Import the read count matrix data into R.
> counts <- as.matrix(read.csv(file.readcounts))
> 
> # Import feature annotations. 
> # Assign feature length into a numeric vector.
> gene.annotations <- read.table(file.annotations, sep="\t", header=TRUE)
> featureLength <- gene.annotations$length
> 
> # Import sample metrics. 
> # Assign mean fragment length into a numeric vector.
> samples.metrics <- read.table(file.sample.metrics, sep="\t", header=TRUE)
> meanFragmentLength <- samples.metrics$meanFragmentLength
> 
> # Return FPKM into a numeric matrix.
> fpkm_matrix <- fpkm (counts, featureLength, meanFragmentLength)
> 
> # Plot log10(FPKM+1) heatmap of top 30 highly variable features
> fpkmheatmap(fpkm_matrix, topvar=30, showfeaturenames=TRUE, return_log = TRUE)
Error: width of the annotation can only be an absolute unit.
Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(covid19us)
  > 
  > test_check("covid19us")
  -- 1. Failure: get_states_daily works (@test-all.R#21)  ------------------------
  nrow(too_early) not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  == testthat results  ===========================================================
  [ OK: 12 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: get_states_daily works (@test-all.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/cp4p.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/cplexAPI.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CSESA.Rcheck/00install.out' for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
Running examples in 'ctDNAtools-Ex.R' failed
The error most likely occurred in:

> ### Name: get_mutations_read_counts
> ### Title: Counts ref and alt reads for a set of mutations
> ### Aliases: get_mutations_read_counts
> 
> ### ** Examples
> 
> data("mutations", package = "ctDNAtools")
> bamT1 <- system.file("extdata", "T1.bam", package = "ctDNAtools")
> get_mutations_read_counts(mutations = mutations[1:3, ], bam = bamT1)
Error: .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ctDNAtools)
  > 
  > test_check("ctDNAtools")
  -- 1. Error: (unknown) (@test-ctDNAtest.R#3)  ----------------------------------
  package 'S4Vectors' could not be loaded
  Backtrace:
   1. base::suppressMessages(library(BSgenome.Hsapiens.UCSC.hg19))
   3. base::library(BSgenome.Hsapiens.UCSC.hg19)
   4. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
   5. base::library(...)
   6. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
  
  -- 2. Error: (unknown) (@test-fragment_size.R#13)  -----------------------------
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
   1. ctDNAtools::get_fragment_size(bamN3)
   2. Rsamtools::scanBamFlag
   3. base::getExportedValue(pkg, name)
   4. base::asNamespace(ns)
   5. base::getNamespace(ns)
   6. base::loadNamespace(name)
   8. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   9. base:::runHook(".onLoad", env, package.lib, package)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: (unknown) (@test-ctDNAtest.R#3) 
  2. Error: (unknown) (@test-fragment_size.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'ctDNAtools.Rmd' using rmarkdown
Quitting from lines 42-69 (ctDNAtools.Rmd) 
Error: processing vignette 'ctDNAtools.Rmd' failed with diagnostics:
package 'S4Vectors' could not be loaded
--- failed re-building 'ctDNAtools.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   4.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.9Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   7.1Mb
File 'curl/libs/i386/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/daqapo.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/dataframeexplorer.Rcheck/00install.out' for details.
.onLoad : <anonymous>: no visible global function definition for
  'read.table'
.onLoad : <anonymous>: no visible global function definition for
  'dbConnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbListTables'
.onLoad : <anonymous>: no visible global function definition for
  'dbExistsTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbReadTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbWriteTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbDisconnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbRemoveTable'
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.1Mb
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:
+   mutate(z = sum(x)) %>%
+   sql_build()
Warning: Missing values are always removed in SQL.
Use `SUM(x, na.rm = TRUE)` to silence this warning
This warning is displayed only once per session.
<SQL SELECT>
From:
  <IDENT> df
Select:   `g`, `y`, SUM(`x`) OVER (PARTITION BY `g` ORDER BY `z` ROWS 3 PRECEDING)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:dplyr'

> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  10.39 0.69 11.18 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 ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DCD.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/dcGOR.Rcheck/00install.out' for details.
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'new'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'new'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'new'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'new'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'new'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava winMenuAdd winMenuAddItem
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DeducerSpatial.Rcheck/00install.out' for details.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   1.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/dGAselID.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DGCA.Rcheck/00install.out' for details.
Running examples in 'dgmb-Ex.R' failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("Tktable") : Tcl package 'Tktable' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "table".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/DiffCorr.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
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:11013 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11013 (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:11753 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11753 (sockconn)
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
Found the following significant warnings:
  Note: possible error in 'glmer(y ~ items + (1 | ': unused argument (REML = FALSE) 
See 'd:/Rcompile/CRANpkg/local/4.0/difR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   2.0Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/dlsem.Rcheck/00install.out' for details.
Running examples in 'dlsem-Ex.R' failed
The error most likely occurred in:

> ### Name: dlsem
> ### Title: Parameter estimation
> ### Aliases: dlsem
> 
> ### ** Examples
> 
> data(industry)
> 
> # Estimation without adaptation of lag shapes
> indus.code <- list(
+   Consum~quec.lag(Job,0,5),
+   Pollution~quec.lag(Job,1,8)+quec.lag(Consum,1,7)
+   )
> indus.mod <- dlsem(indus.code,group="Region",time="Year",exogenous=c("Population","GDP"),
+   data=industry,log=TRUE)
Checking stationarity ...
Order 1 differentiation performed 
Starting estimation ...
Estimating regression 1/3 (Job)
Estimating regression 2/3 (Consum)
Estimating regression 3/3 (Pollution)
Estimation completed                   
> 
> # Adaptation of lag shapes (estimation takes some seconds more)
> indus.global <- list(adapt=TRUE,max.gestation=5,max.lead=15,min.width=3,sign="+")
> ## NOT RUN:
> # indus.mod <- dlsem(indus.code,group="Region",time="Year",exogenous=c("Population","GDP"),
> #   data=industry,global.control=indus.global,log=TRUE)
> 
> # Summary of estimation
> summary(indus.mod)$endogenous
$Job
NULL

$Consum
                             Estimate Std. Error  t value     Pr(>|t|)    
quec.lag(Job, 0, 5, Region) 0.1006394 0.01679967 5.990556 7.347355e-09 ***

$Pollution
                                 Estimate Std. Error  t value     Pr(>|t|)    
quec.lag(Job, 1, 8, Region)    0.08925573 0.03120937 2.859902 4.653304e-03  **
quec.lag(Consum, 1, 7, Region) 0.24416273 0.03430066 7.118310 1.593832e-11 ***

> 
> # DAG with coloured edges
> plot(indus.mod)
Error in as.double(x) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot ... plot.dlsem -> plot -> plot -> plot.default -> xy.coords
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:
   <int> <chr> <chr>
 1  2013 1     10   
 2  2013 1     10   
 3  2013 1     10   
 4  2013 1     10   
 5  2013 1     10   
 6  2013 1     10   
 7  2013 1     10   
 8  2013 1     10   
 9  2013 1     10   
10  2013 1     10   
# ... with 11,217 more rows
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  32.05 0.89 33.3 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 'DMwR2-Ex.R' failed
The error most likely occurred in:

> ### Name: centralImputation
> ### Title: Fill in NA values with central statistics
> ### Aliases: centralImputation
> ### Keywords: models
> 
> ### ** Examples
> 
> data(algae,package="DMwR2")
> cleanAlgae <- centralImputation(algae)
Error: `i` must have one dimension, not 2.
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/dnet.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.5Mb
Error(s) in re-building vignettes:
--- re-building 'dodgr.Rmd' using rmarkdown
Quitting from lines 323-330 (dodgr.Rmd) 
Error: processing vignette 'dodgr.Rmd' failed with diagnostics:
`x` must be a vector, not a `sfc_LINESTRING/sfc` object.
--- failed re-building 'dodgr.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DRomics.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/dSVA.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'aws'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   5.0Mb
Running 'testthat.R' [35s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dyndimred)
  > library(dynutils)
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  > 
  > test_check("dyndimred")
  -- 1. Error: Perform dimred dm_destiny  ----------------------------------------
  Please install the following packages: 
    "destiny"
  Backtrace:
   1. dyndimred:::method_fun(expr)
   2. dynutils::install_packages("destiny")
  
  -- 2. Error: Perform dimred dm_destiny  ----------------------------------------
  Please install the following packages: 
    "destiny"
  Backtrace:
   1. dyndimred:::method_fun(small_expr)
   2. dynutils::install_packages("destiny")
  
  == testthat results  ===========================================================
  [ OK: 191 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 2 ]
  1. Error: Perform dimred dm_destiny 
  2. Error: Perform dimred dm_destiny 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   1.2Mb
Running examples in 'eclust-Ex.R' failed
The error most likely occurred in:

> ### Name: s_generate_data
> ### Title: Generate linear response data and test and training sets for
> ###   simulation study
> ### Aliases: s_generate_data
> 
> ### ** Examples
> 
> library(magrittr)
> 
> # simulation parameters
> rho = 0.90; p = 500 ;SNR = 1 ; n = 200; n0 = n1 = 100 ; nActive = p*0.10 ; cluster_distance = "tom";
> Ecluster_distance = "difftom"; rhoOther = 0.6; betaMean = 2;
> alphaMean = 1; betaE = 3; distanceMethod = "euclidean"; clustMethod = "hclust";
> cutMethod = "dynamic"; agglomerationMethod = "average"
> 
> #in this simulation its blocks 3 and 4 that are important
> #leaveOut:  optional specification of modules that should be left out
> #of the simulation, that is their genes will be simulated as unrelated
> #("grey"). This can be useful when simulating several sets, in some which a module
> #is present while in others it is absent.
> d0 <- s_modules(n = n0, p = p, rho = 0, exposed = FALSE,
+                 modProportions = c(0.15,0.15,0.15,0.15,0.15,0.25),
+                 minCor = 0.01,
+                 maxCor = 1,
+                 corPower = 1,
+                 propNegativeCor = 0.3,
+                 backgroundNoise = 0.5,
+                 signed = FALSE,
+                 leaveOut = 1:4)
Error: .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Execution halted
Error(s) in re-building vignettes:
--- re-building 'eclust.Rmd' using rmarkdown
See example usage at http://sahirbhatnagar.com/eclust/
Quitting from lines 142-168 (eclust.Rmd) 
Error: processing vignette 'eclust.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
--- failed re-building 'eclust.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: replacing previous import 'sf::st_make_valid' by 'lwgeom::st_make_valid' when loading 'edbuildmapr'
See 'd:/Rcompile/CRANpkg/local/4.0/edbuildmapr.Rcheck/00install.out' for details.
Running 'test-all.R' [13s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  -- 1. Failure: moves_calc gets the correct results (@test-calculators.R#210)  --
  `moves` not equal to `correct_result`.
  Component "sid": Modes: character, numeric
  Component "sid": Attributes: < target is NULL, current is list >
  Component "sid": target is character, current is factor
  
  == testthat results  ===========================================================
  [ OK: 509 | SKIPPED: 0 | WARNINGS: 29 | FAILED: 1 ]
  1. Failure: moves_calc gets the correct results (@test-calculators.R#210) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Running examples in 'eixport-Ex.R' failed
The error most likely occurred in:

> ### Name: sfx_explode
> ### Title: splits line by vertex
> ### Aliases: sfx_explode
> 
> ### ** Examples
> 
> {
+ # Do not run
+ data(emisco)
+ emisco <- emisco[1:100, "V8"]
+ dfco <- sfx_explode(emisco)
+ etm <- to_munich(sdf = dfco)
+ names(etm)
+ class(etm)
+ head(etm$Emissions)
+ head(etm$Street)
+ write.table(x = etm$Emissions, file = paste0(tempfile(), "_Emissions.txt"),
+ row.names = FALSE, sep = " ", quote = FALSE)
+ write.table(x = etm$Street, file = paste0(tempfile(), "_Street.txt"),
+ row.names = FALSE, sep = " ", quote = FALSE)
+ }
Error in to_munich(sdf = dfco) : 
  All emissions must have units. Check ?units::set_units
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/EMA.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    extdata  10.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/empiricalFDR.DESeq2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/EncDNA.Rcheck/00install.out' for details.
Running examples in 'enviGCMS-Ex.R' failed
The error most likely occurred in:

> ### Name: getpower
> ### Title: Get the index with power restriction for certain study with BH
> ###   adjusted p-value and certain power.
> ### Aliases: getpower
> 
> ### ** Examples
> 
> data(list)
> getpower(list)
Error: .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(epikit)
  > 
  > test_check("epikit")
  -- 1. Failure: case_fatality_rate_df will add a total row to stratified analysis
  `iris_res` not equal to `iris_n`.
  Incompatible type for column `Species`: x character, y factor
  
  -- 2. Failure: case_fatality_rate_df will add a total row to stratified analysis
  `iris_res` not equal to `iris_n`.
  Incompatible type for column `Species`: x character, y factor
  
  == testthat results  ===========================================================
  [ OK: 107 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: case_fatality_rate_df will add a total row to stratified analysis (@test-proportion.R#152) 
  2. Failure: case_fatality_rate_df will add a total row to stratified analysis and merge CI (@test-proportion.R#173) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'eqn2svg-Ex.R' failed
The error most likely occurred in:

> ### Name: eqn2svg
> ### Title: Convert a LaTeX math formula to an SVG object
> ### Aliases: eqn2svg
> 
> ### ** Examples
> 
> # Take LaTeX code for the Heaviside
> # Function and convert that to SVG
> heaviside <-
+   eqn2svg(
+     eqn = l_time_domain[25],
+     preview = FALSE
+   )
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: eqn2svg -> readLines -> file
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eqn2svg)
  > 
  > test_check("eqn2svg")
  -- 1. Error: SVG conversion works (@test-eqn2svg.R#3)  -------------------------
  cannot open the connection
  Backtrace:
   1. eqn2svg::eqn2svg(eqn = l_time_domain[25], preview = FALSE)
   2. base::readLines(url, warn = FALSE)
   3. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: SVG conversion works (@test-eqn2svg.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(estatapi)
  <U+3053><U+306E><U+30B5><U+30FC><U+30D3><U+30B9><U+306F><U+3001><U+653F><U+5E9C><U+7D71><U+8A08><U+7DCF><U+5408><U+7A93><U+53E3>(e-Stat)<U+306E>API<U+6A5F><U+80FD><U+3092><U+4F7F><U+7528><U+3057><U+3066><U+3044><U+307E><U+3059><U+304C><U+3001><U+30B5><U+30FC><U+30D3><U+30B9><U+306E><U+5185><U+5BB9><U+306F><U+56FD><U+306B><U+3088><U+3063><U+3066><U+4FDD><U+8A3C><U+3055><U+308C><U+305F><U+3082><U+306E><U+3067><U+306F><U+3042><U+308A><U+307E><U+305B><U+3093><U+3002>
  > 
  > test_check("estatapi")
  -- 1. Failure: estat_getStatsData processes the API response as expected  ------
  estat_getStatsData(...) not identical to readRDS("result_getStatsData.rds").
  Objects equal but not identical
  
  == testthat results  ===========================================================
  [ OK: 22 | SKIPPED: 12 | WARNINGS: 7 | FAILED: 1 ]
  1. Failure: estat_getStatsData processes the API response as expected 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'etm-Ex.R' failed
The error most likely occurred in:

> ### Name: etm
> ### Title: Computation of the empirical transition matrix
> ### Aliases: etm etm.data.frame
> ### Keywords: survival
> 
> ### ** Examples
> 
> data(sir.cont)
> 
> # Modification for patients entering and leaving a state
> # at the same date
> # Change on ventilation status is considered
> # to happen before end of hospital stay
> sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ]
> for (i in 2:nrow(sir.cont)) {
+   if (sir.cont$id[i]==sir.cont$id[i-1]) {
+     if (sir.cont$time[i]==sir.cont$time[i-1]) {
+       sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5
+     }
+   }
+ }
> 
> ### Computation of the transition probabilities
> # Possible transitions.
> tra <- matrix(ncol=3,nrow=3,FALSE)
> tra[1, 2:3] <- TRUE
> tra[2, c(1, 3)] <- TRUE
> 
> # etm
> tr.prob <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1)
> 
> tr.prob
Multistate model with 3 transient state(s)
 and 0 absorbing state(s)

Possible transitions:
 from to
    0  1
    0  2
    1  0
    1  2

Estimate of P(1, 183)
  0 1 2
0 0 0 1
1 0 0 1
2 0 0 1

> summary(tr.prob)
Error in object$n.risk[, trs.sep[i, 1]] : subscript out of bounds
Calls: summary -> summary.etm -> ci.transfo -> lapply -> FUN
Execution halted
Error(s) in re-building vignettes:
--- re-building 'etmCIF_tutorial.Rnw' using Sweave
Error: processing vignette 'etmCIF_tutorial.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building 'etmCIF_tutorial.Rnw'

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

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

> ### Name: exposure_histogram
> ### Title: Display a histogram of losses for a scenario
> ### Aliases: exposure_histogram
> 
> ### ** Examples
> 
> data(mc_simulation_results)
> result <- mc_simulation_results[[1, "results"]]
> exposure_histogram(result)
Error: `data` must be a data frame, or other object coercible by `fortify()`, not a list
Backtrace:
    x
 1. \-evaluator::exposure_histogram(result)
 2.   +-ggplot2::ggplot(simulation_result, aes(x = .data$ale))
 3.   \-ggplot2:::ggplot.default(simulation_result, aes(x = .data$ale))
 4.     +-ggplot2::fortify(data, ...)
 5.     \-ggplot2:::fortify.default(data, ...)
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ExomeDepth.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/exp2flux.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'using_genExPrior.Rmd' using rmarkdown
Quitting from lines 58-59 (using_genExPrior.Rmd) 
Error: processing vignette 'using_genExPrior.Rmd' failed with diagnostics:
unable to load shared object 'D:/temp/RtmpwNeCBb/nimble_generatedCode/dynamicRegistrations_04_09_01_00_28.dll':
  LoadLibrary failure:  Das angegebene Modul wurde nicht gefunden.

--- failed re-building 'using_genExPrior.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [37s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(fable)
  Loading required package: fabletools
  > 
  > test_check("fable")
  -- 1. Failure: Automatic ETS selection (@test-ets.R#14)  -----------------------
  tidy(model(UKLungDeaths[1:24, ], ETS(mdeaths)))$estimate not equal to c(1, 2134).
  names for target but not for current
  
  -- 2. Failure: Manual ETS selection (@test-ets.R#51)  --------------------------
  tidy(refit(fable_fit, USAccDeaths_tbl))$estimate == tidy(fable_fit)$estimate not identical to c(rep(TRUE, 2), rep(FALSE, 12)).
  names for target but not for current
  
  -- 3. Failure: Manual ETS selection (@test-ets.R#62)  --------------------------
  tidy(fable_fit)$estimate[3:14] not identical to c(cmp$level[12], cmp$season[12:2]).
  names for target but not for current
  
  -- 4. Failure: Manual ETS selection (@test-ets.R#87)  --------------------------
  coef$estimate[1:4] not identical to c(0.5, 0.006, 1e-04, 0.975).
  names for target but not for current
  
  == testthat results  ===========================================================
  [ OK: 100 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Automatic ETS selection (@test-ets.R#14) 
  2. Failure: Manual ETS selection (@test-ets.R#51) 
  3. Failure: Manual ETS selection (@test-ets.R#62) 
  4. Failure: Manual ETS selection (@test-ets.R#87) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(fable)
  Loading required package: fabletools
  > 
  > test_check("fable")
  -- 1. Failure: Automatic ETS selection (@test-ets.R#14)  -----------------------
  tidy(model(UKLungDeaths[1:24, ], ETS(mdeaths)))$estimate not equal to c(1, 2134).
  names for target but not for current
  
  -- 2. Failure: Manual ETS selection (@test-ets.R#51)  --------------------------
  tidy(refit(fable_fit, USAccDeaths_tbl))$estimate == tidy(fable_fit)$estimate not identical to c(rep(TRUE, 2), rep(FALSE, 12)).
  names for target but not for current
  
  -- 3. Failure: Manual ETS selection (@test-ets.R#62)  --------------------------
  tidy(fable_fit)$estimate[3:14] not identical to c(cmp$level[12], cmp$season[12:2]).
  names for target but not for current
  
  -- 4. Failure: Manual ETS selection (@test-ets.R#87)  --------------------------
  coef$estimate[1:4] not identical to c(0.5, 0.006, 1e-04, 0.975).
  names for target but not for current
  
  == testthat results  ===========================================================
  [ OK: 100 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Automatic ETS selection (@test-ets.R#14) 
  2. Failure: Manual ETS selection (@test-ets.R#51) 
  3. Failure: Manual ETS selection (@test-ets.R#62) 
  4. Failure: Manual ETS selection (@test-ets.R#87) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
File 'fastmatch/libs/i386/fastmatch.dll':
  Found non-API call to R: 'match5'
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Error(s) in re-building vignettes:
--- re-building 'FateID.Rmd' using rmarkdown
Quitting from lines 141-142 (FateID.Rmd) 
Error: processing vignette 'FateID.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
--- failed re-building 'FateID.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/fcaR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/FcircSEC.Rcheck/00install.out' for details.
Running examples in 'ff-Ex.R' failed
The error most likely occurred in:

> ### Name: Extract.ffdf
> ### Title: Reading and writing data.frames (ffdf)
> ### Aliases: Extract.ffdf [.ffdf [<-.ffdf [[.ffdf [[<-.ffdf $.ffdf $<-.ffdf
> ### Keywords: IO data
> 
> ### ** Examples
> 
>    d <- data.frame(a=letters, b=rev(letters), c=1:26)
>    x <- as.ffdf(d)
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered,  : 
  vmode 'character' not implemented
Calls: as.ffdf ... do.call -> as.ff -> as.ff.default -> clone.ff -> assign -> ff
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   1.7Mb
Packages suggested but not available for checking: 'doMC', 'RSvgDevice'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.8Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R   6.3Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/flowDiv.Rcheck/00install.out' for details.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/foreign.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.5Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(fredr)
  > 
  > test_check("fredr")
  -- 1. Failure: fredr_docs throws errors on invalid endpoints (@test_docs.R#8)  -
  `fredr_docs(endpoint = "foo")` did not throw an error.
  
  -- 2. Failure: fredr_docs throws errors on invalid endpoints (@test_docs.R#9)  -
  `fredr_docs(endpoint = "foo", params = TRUE)` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 65 | SKIPPED: 38 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: fredr_docs throws errors on invalid endpoints (@test_docs.R#8) 
  2. Failure: fredr_docs throws errors on invalid endpoints (@test_docs.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(freetypeharfbuzz)
  > 
  > test_check("freetypeharfbuzz")
  -- 1. Failure: string metrics are computed for various edge cases (@test-string-
  `metrics` not equal to c(width = w, height = h, ascent = a, descent = d).
  2/4 mismatches (average diff: 1e-04)
  [2] 1.28 - 1.28 == 1e-04
  [3] 1.28 - 1.28 == 1e-04
  
  == testthat results  ===========================================================
  [ OK: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: string metrics are computed for various edge cases (@test-string-info.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'dggrids'
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.4Mb
    libs   1.4Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/funbarRF.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      1.5Mb
Running 'testthat.R' [25s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(fuzzyjoin)
  > 
  > test_check("fuzzyjoin")
  -- 1. Failure: genome_join throws an error if not given three columns (@test_gen
  `genome_inner_join(x1, x2, by = c("start", "end"))` threw an error with unexpected message.
  Expected match: "three columns"
  Actual message: "genome_join requires the IRanges package: https://bioconductor.org/packages/release/bioc/html/IRanges.html"
  Backtrace:
   1. testthat::expect_error(...)
   6. fuzzyjoin::genome_inner_join(x1, x2, by = c("start", "end"))
   7. fuzzyjoin::genome_join(x, y, by, mode = "inner", ...)
  
  == testthat results  ===========================================================
  [ OK: 230 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: genome_join throws an error if not given three columns (@test_genome_join.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/g2f.Rcheck/00install.out' for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
finterp.data.frame: no visible global function definition for
  'as.formula'
finterp.data.frame: no visible global function definition for 'terms'
finterp.data.frame: no visible global function definition for
  'model.matrix'
finterp.data.frame: no visible global function definition for
  'model.frame'
finterp.default: no visible global function definition for 'terms'
finterp.default: no visible global function definition for
  'model.matrix'
finterp.default: no visible global function definition for
  'model.frame'
gamlss.nl: no visible global function definition for 'nlm'
nl: no visible global function definition for 'is'
nlgamlss: no visible global function definition for 'NO'
nlgamlss: no visible global function definition for 'as.gamlss.family'
nlgamlss: no visible global function definition for 'nlm'
nlgamlss: no visible global function definition for 'cov2cor'
summary.nlgamlss: no visible global function definition for 'coef'
summary.nlgamlss: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.8Mb
installed size is 84.5Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    gdal     3.8Mb
    libs    72.1Mb
    proj     5.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R  10.2Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/geneNetBP.Rcheck/00install.out' for details.
Warnings in file 'R/utils.R':
  unable to translate '<U+00E9>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+2019>' to native encoding
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/geno2proteo.Rcheck/00install.out' for details.
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R         8.9Mb
    extdata   1.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   3.5Mb
Running examples in 'germanpolls-Ex.R' failed
The error most likely occurred in:

> ### Name: germanpolls
> ### Title: Get data of German polls from wahlrecht.de.
> ### Aliases: germanpolls
> 
> ### ** Examples
> 
> germanpolls(region = "de")
[1] "http://www.wahlrecht.de/umfragen/bundesweite.xml"
 [1] "datum"    "institut" "gebiet"   "cxu"      "spd"      "grn"     
 [7] "fpd"      "lnk"      "afd"      "pir"      "frw"      "son"     
[13] "befragte" "gerundet" "beginn"   "ende"     "methode"  "art_ag"  
[19] "ag_1"     "ag_2"     "status"   "stand"   
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error: All columns in a tibble must be vectors.
x Column `node` is a `xml_nodeset` object.
Backtrace:
    x
 1. \-germanpolls::germanpolls(region = "de")
 2.   \-germanpolls::get_data_from_xml_de()
 3.     \-tibble::data_frame(row = seq_along(rows), node = rows)
 4.       \-tibble::tibble(!!!quos(...))
 5.         \-tibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
 6.           \-tibble:::check_valid_col(res, col_names[[j]], j)
 7.             \-tibble:::check_valid_cols(set_names(list(x), name))
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/GExMap.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'ggalluvial.rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: ggplot2
Quitting from lines 36-46 (ggalluvial.rmd) 
Error: processing vignette 'ggalluvial.rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building 'ggalluvial.rmd'

--- re-building 'labels.rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 31-40 (labels.rmd) 
Error: processing vignette 'labels.rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building 'labels.rmd'

--- re-building 'order-rectangles.rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 43-46 (order-rectangles.rmd) 
Error: processing vignette 'order-rectangles.rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building 'order-rectangles.rmd'

SUMMARY: processing the following files failed:
  'ggalluvial.rmd' 'labels.rmd' 'order-rectangles.rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ggmsa.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ggtern.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    doc         1.2Mb
    libs       21.2Mb
    test_data   1.2Mb
plot.glmulti: no visible global function definition for 'windows'
glmulti,character-character-ANY-ANY: no visible global function
  definition for 'regsubsets'
Undefined global functions or variables:
  regsubsets windows
Consider adding
  importFrom("grDevices", "windows")
to your NAMESPACE file.
Package suggested but not available for checking: 'cplexAPI'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/GMMAT.Rcheck/00install.out' for details.
File 'gnmf/libs/i386/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'
File 'gnmf/libs/x64/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/GOGANPA.Rcheck/00install.out' for details.
gpairs: no visible global function definition for 'hclust'
gpairs: no visible global function definition for 'dist'
gpairs : scatterplot.panel: no visible global function definition for
  'lm'
gpairs : scatterplot.panel: no visible global function definition for
  'predict'
gpairs : scatterplot.panel: no visible global function definition for
  'prcomp'
gpairs : scatterplot.panel: no visible global function definition for
  'cor'
gpairs : scatterplot.panel: no visible global function definition for
  'cor.test'
gpairs : scatterplot.panel: no visible global function definition for
  'hsv'
gpairs : scatterplot.panel: no visible global function definition for
  'na.omit'
gpairs : scatterplot.panel: no visible global function definition for
  'pf'
gpairs : scatterplot.panel: no visible global function definition for
  'grey'
Undefined global functions or variables:
  cor cor.test dist grey hclust hsv lm na.omit pf prcomp predict
Consider adding
  importFrom("grDevices", "grey", "hsv")
  importFrom("stats", "cor", "cor.test", "dist", "hclust", "lm",
             "na.omit", "pf", "prcomp", "predict")
to your NAMESPACE file.
Running examples in 'gpairs-Ex.R' failed
The error most likely occurred in:

> ### Name: gpairs
> ### Title: Generalized Pairs Plots
> ### Aliases: gpairs corrgram
> ### Keywords: ts multivariate
> 
> ### ** Examples
> 
> 
> allexamples <- FALSE
> 
> y <- data.frame(A=c(rep("red", 100), rep("blue", 100)),
+                 B=c(rnorm(100),round(rnorm(100,5,1),1)), C=runif(200),
+                 D=c(rep("big", 150), rep("small", 50)),
+                 E=rnorm(200))
> gpairs(y)
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in max(as.numeric(x), na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in min(as.numeric(x), na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in max(as.numeric(x), na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in min(as.numeric(x), na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
Error in valid.viewport(x, y, width, height, just, gp, clip, xscale, yscale,  : 
  invalid 'xscale' in viewport
Calls: gpairs ... diag.panel -> pushViewport -> viewport -> valid.viewport
Execution halted
Warning: no function found corresponding to methods exports from 'gpclib' for: 'coerce', 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
read.polyfile: no visible global function definition for 'as'
write.polyfile: no visible global function definition for 'is'
write.polyfile: no visible global function definition for 'as'
[,gpc.poly: no visible global function definition for 'new'
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for 'new'
coerce,data.frame-gpc.poly: no visible global function definition for
  'as'
coerce,list-gpc.poly: no visible global function definition for 'as'
coerce,matrix-gpc.poly: no visible global function definition for 'new'
coerce,numeric-gpc.poly: no visible global function definition for
  'new'
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for 'new'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'as'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'new'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'as'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'new'
tristrip,gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for
  'new'
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'bug1.R' [1s]
  Running 'reg-tests.R' [1s]
  Comparing 'reg-tests.Rout' to 'reg-tests.Rout.save' ...58c58
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
68c68
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
83c83
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
Running the tests in 'tests/bug1.R' failed.
Complete output:
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/gpuR.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/gRain.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'grain-intro.Rnw' using knitr
Warning in dir.create("figures") : 'figures' already exists
Loading required package: gRain
Loading required package: gRbase
Warning: multiple methods tables found for 'plot'
Warning: multiple methods tables found for 'plot'
Quitting from lines 139-140 (grain-intro.Rnw) 
Error: processing vignette 'grain-intro.Rnw' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'grain-intro.Rnw'

SUMMARY: processing the following file failed:
  'grain-intro.Rnw'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/graphicalVAR.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/gRbase.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'arrays.Rnw' using knitr
--- finished re-building 'arrays.Rnw'

--- re-building 'graphs.Rnw' using knitr
Quitting from lines 216-220 (graphs.Rnw) 
Error: processing vignette 'graphs.Rnw' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'graphs.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/gRc.Rcheck/00install.out' for details.
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/r-reticulate/python.exe" "d:/RCompile/CRANpkg/lib/4.0/reticulate/config/config.py"' had status 2

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.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/gridDebug.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/gridGraphviz.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/gRim.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'dse1'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/gtools.Rcheck/00install.out' for details.
Running examples in 'GuardianR-Ex.R' failed
The error most likely occurred in:

> ### Name: get_guardian
> ### Title: Search Guardian API for news articles that match the criteria
> ### Aliases: get_guardian
> ### Keywords: IO utilities
> 
> ### ** Examples
> 
> ## Not run:
> results <- get_guardian("islamic+state", 
+ 	section="world",
+ 	from.date="2014-09-16", 
+ 	to.date="2014-09-16", 
+ 	api.key="212d23d3-c7b2-4273-8f1b-289a0803ca4b")
trying URL 'https://curl.haxx.se/ca/cacert.pem'
Warning in download.file(url = "https://curl.haxx.se/ca/cacert.pem", destfile = "cacert.perm") :
  InternetOpenUrl failed: ''
Error in download.file(url = "https://curl.haxx.se/ca/cacert.pem", destfile = "cacert.perm") : 
  cannot open URL 'https://curl.haxx.se/ca/cacert.pem'
Calls: get_guardian -> get_json -> download.file
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/GUIProfiler.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial") 
See 'd:/Rcompile/CRANpkg/local/4.0/GWAF.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
normalweight: no visible binding for global variable 'NW_above'
normalweight: no visible binding for global variable 'NW_below'
obese: no visible global function definition for 'data'
obese: no visible binding for global variable 'OB_above'
obese: no visible binding for global variable 'OB_below'
overweight: no visible global function definition for 'data'
overweight: no visible binding for global variable 'OW_above'
overweight: no visible binding for global variable 'OW_below'
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 134.3Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    java  132.1Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/hasseDiagram.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/hddplot.Rcheck/00install.out' for details.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.5Mb
    CWrappers_1.10.3   2.4Mb
    CWrappers_1.12.0   2.8Mb
    libs               6.7Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/HDMT.Rcheck/00install.out' for details.
Running examples in 'heemod-Ex.R' failed
The error most likely occurred in:

> ### Name: define_dsa
> ### Title: Define a Sensitivity Analysis
> ### Aliases: define_dsa define_dsa_
> 
> ### ** Examples
> 
> 
> define_dsa(
+   a, 10, 45,
+   b, .5, 1.5
+ )
Error: All columns in a tibble must be vectors.
x Column `dots[i]` is a `lazy_dots` object.
Backtrace:
     x
  1. \-heemod::define_dsa(a, 10, 45, b, 0.5, 1.5)
  2.   \-heemod:::define_dsa_(...)
  3.     +-base::suppressWarnings(...)
  4.     | \-base::withCallingHandlers(...)
  5.     +-dplyr::bind_rows(...)
  6.     | +-dplyr:::flatten_bindable(dots_values(...))
  7.     | \-rlang::dots_values(...)
  8.     +-stats::setNames(tibble::tibble(dots[i]), names(dots)[i])
  9.     \-tibble::tibble(dots[i])
 10.       \-tibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
 11.         \-tibble:::check_valid_col(res, col_names[[j]], j)
 12.           \-tibble:::check_valid_cols(set_names(list(x), name))
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/HeritSeq.Rcheck/00install.out' for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/HiCfeat.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
    libs   1.5Mb
PlotOptPower: no visible global function definition for 'bmp'
PlotOptPower: no visible global function definition for
  'filled.contour'
PlotOptPower: no visible global function definition for 'title'
PlotOptPower: no visible global function definition for 'grey.colors'
PlotOptPower: no visible global function definition for 'axis'
PlotOptPower: no visible global function definition for 'polygon'
PlotOptPower: no visible global function definition for 'legend'
PlotOptPower: no visible global function definition for 'mtext'
PlotOptPower: no visible global function definition for 'dev.off'
PlotOptPower: no visible global function definition for
  'terrain.colors'
ShowOptDesign: no visible global function definition for 'head'
diffVariantError: no visible global function definition for 'pbinom'
predictPoolNCP: no visible global function definition for 'data'
probDetEqual3: no visible global function definition for 'dbinom'
probDetEqual3: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/hoardeR.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/hpoPlot.Rcheck/00install.out' for details.
Running examples in 'hpoPlot-Ex.R' failed
The error most likely occurred in:

> ### Name: hpo.plot
> ### Title: Plot HPO graph object
> ### Aliases: hpo.plot
> 
> ### ** Examples
> 
> data(hpo.terms)
> hpo.plot(
+ 	hpo.terms=hpo.terms,
+ 	terms=get.ancestors(hpo.terms, 
+ 	c("HP:0001382","HP:0004272","HP:0007917","HP:0004912","HP:0001596"))
+ )
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: hpo.plot -> plot -> plot -> plot.default -> xy.coords
Execution halted
Error(s) in re-building vignettes:
--- re-building 'hpoPlot-guide.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 23-24 (hpoPlot-guide.Rmd) 
Error: processing vignette 'hpoPlot-guide.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'hpoPlot-guide.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Error in .requirePackage(package) : 
  unable to find required package 'phyloseq'
Calls: <Anonymous> ... withCallingHandlers -> is -> getClassDef -> .requirePackage
Execution halted
Error loading dataset 'physeq_S2D1':
   Error in .requirePackage(package) : 
    unable to find required package 'phyloseq'
  
  Error loading dataset 'physeq_S2D1_l':
   Error in .requirePackage(package) : 
    unable to find required package 'phyloseq'
  
  Error loading dataset 'physeq_S2D2':
   Error in .requirePackage(package) : 
    unable to find required package 'phyloseq'
  
  Error loading dataset 'physeq_S2D2_l':
   Error in .requirePackage(package) : 
    unable to find required package 'phyloseq'
  
  Error loading dataset 'physeq_rep3':
   Error in .requirePackage(package) : 
    unable to find required package 'phyloseq'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
Running examples in 'HTSSIP-Ex.R' failed
The error most likely occurred in:

> ### Name: OTU_qPCR_trans
> ### Title: Transform OTU counts based on qPCR data
> ### Aliases: OTU_qPCR_trans
> 
> ### ** Examples
> 
> # qPCR data simulation
> data(physeq_rep3)
> data(physeq_rep3_qPCR)
> physeq_rep3_t = OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR)
Error: .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Execution halted
Error(s) in re-building vignettes:
--- re-building 'DecisionNetworks.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: nnet
--- finished re-building 'DecisionNetworks.Rmd'

--- re-building 'GettingStartedWithHydeNet.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'GettingStartedWithHydeNet.Rmd'

--- re-building 'HydeNetPlots.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 158-167 (HydeNetPlots.Rmd) 
Error: processing vignette 'HydeNetPlots.Rmd' failed with diagnostics:
Blackjack rules URL does not exist.  Find a new link
--- failed re-building 'HydeNetPlots.Rmd'

--- re-building 'WorkingWithHydeNetObjects.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'WorkingWithHydeNetObjects.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ICAMS.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ICDS.Rcheck/00install.out' for details.
Running examples in 'icrf-Ex.R' failed
The error most likely occurred in:

> ### Name: measure
> ### Title: Prediction error measures
> ### Aliases: measure
> 
> ### ** Examples
> 
> # rats data example.
> # Note that this is a toy example. Use a larger ntree and nfold in practice.
> library(survival)  # for Surv()
> data(rat2)
> L = ifelse(rat2$tumor, 0, rat2$survtime)
> R = ifelse(rat2$tumor, rat2$survtime, Inf)
> ## Don't show: 
> set.seed(2)
> 
> rats.icrf <-
+   icrf(Surv(L, R, type = "interval2") ~ dose.lvl + weight + male + cage.no,
+        data = rat2, ntree = 2, nfold = 2)

Forest loop 1 out of 2 folds
Tree 1 2 
   IMSE1 (OOB, non-OOB) = (0.000, 0.000), IMSE2 = (nan, nan)
Forest loop 2 out of 2 folds
Tree 1 2 
   IMSE1 (OOB, non-OOB) = (0.000, 0.000), IMSE2 = (nan, nan)
> 
> measure(rats.icrf$predicted.Sm, timepoints = rats.icrf$time.points,
+         tau = rats.icrf$tau, method = "imse", L = L, R = R)
Error in measure(rats.icrf$predicted.Sm, timepoints = rats.icrf$time.points,  : 
  NA/NaN/Inf in foreign function call (arg 2)
Execution halted
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/iheatmapr.Rcheck/00install.out' for details.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     15.3Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/IMaGES.Rcheck/00install.out' for details.
Running examples in 'IMaGES-Ex.R' failed
The error most likely occurred in:

> ### Name: IMData
> ### Title: IMaGES Test Data
> ### Aliases: IMData
> ### Keywords: data
> 
> ### ** Examples
> 
> data(IMData)
> 
> result <- IMaGES(matrices=IMData)
[1] "Running..."
[1] "Stopping early. IMaGES run has converged on a representative graph."
[1] "Done with IMaGES run."
[1] "Final IMScore:  220936.078265306"
> 
> plotAll(result)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plotAll ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
Running examples in 'IMaGES-Ex.R' failed
The error most likely occurred in:

> ### Name: IMData
> ### Title: IMaGES Test Data
> ### Aliases: IMData
> ### Keywords: data
> 
> ### ** Examples
> 
> data(IMData)
> 
> result <- IMaGES(matrices=IMData)
[1] "Running..."
[1] "Stopping early. IMaGES run has converged on a representative graph."
[1] "Done with IMaGES run."
[1] "Final IMScore:  220936.078265305"
> 
> plotAll(result)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plotAll ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
Error(s) in re-building vignettes:
--- re-building 'IMaGES.Rmd' using rmarkdown
Warning: multiple methods tables found for 'plot'
Quitting from lines 119-131 (IMaGES.Rmd) 
Error: processing vignette 'IMaGES.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'IMaGES.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/immuneSIM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/INCATome.Rcheck/00install.out' for details.
Running examples in 'INDperform-Ex.R' failed
The error most likely occurred in:

> ### Name: merge_models
> ### Title: Merging two model output tibbles.
> ### Aliases: merge_models
> 
> ### ** Examples
> 
> # Using some models of the Baltic Sea demo data:
> # Merging GAM and GAMM tibbles
> test_ids <- 47:50 # choose subset
> gam_tbl <- model_gam_ex[test_ids,]
> gamm_tbl <- model_gamm(ind_init_ex[test_ids,], filter= gam_tbl$tac)
Error in model_gamm(ind_init_ex[test_ids, ], filter = gam_tbl$tac) : 
  No IND~pressure GAMM could be fitted! Check if you chose the correct error distribution (default is gaussian()).
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/intePareto.Rcheck/00install.out' for details.
ClearBottomMenuPlot: no visible global function definition for 'rect'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertX'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertX'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'polygon'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertX'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertY'
InteractiveIGraph : keybd: no visible global function definition for
  'readClipboard'
InteractiveIGraph : keybd: no visible global function definition for
  'par'
PlotRegionGeneral: no visible global function definition for 'polygon'
plot.InteractiveIGraph: no visible global function definition for 'par'
plot.Menu: no visible global function definition for 'par'
plot.Menu: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'strwidth'
plot.MenuItem: no visible binding for global variable 'strheight'
plot.MenuItem: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'text'
plot.MenuLine: no visible binding for global variable 'rect'
Undefined global functions or variables:
  grconvertX grconvertY par polygon readClipboard rect strheight
  strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "polygon",
             "rect", "strheight", "strwidth", "text")
  importFrom("utils", "readClipboard")
to your NAMESPACE file.
Interpol: no visible global function definition for 'splinefun'
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ionflows.Rcheck/00install.out' for details.
File 'iotools/libs/i386/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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] 293
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11935 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11935 (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:11212 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11212 (sockconn)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Loading required package: pkgmaker
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
# NOTE - CRAN check detected: limiting maximum number of cores [2/32]
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 2/2 | CRAN check
Loading required namespace: Rgraphviz
Quitting from lines 94-99 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'acf.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'acf.Rmd'

--- re-building 'inspect.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 101-106 (inspect.Rmd) 
Error: processing vignette 'inspect.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building 'inspect.Rmd'

--- re-building 'test.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 187-200 (test.Rmd) 
Error: processing vignette 'test.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building 'test.Rmd'

SUMMARY: processing the following files failed:
  'inspect.Rmd' 'test.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           8.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/janitor.Rcheck/00install.out' for details.
Package unavailable to check Rd xrefs: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/jetset.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/kangar00.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.9Mb
comp.npci: no visible global function definition for 'qnorm'
epband.fun: no visible global function definition for 'data'
epband.fun: no visible binding for global variable
  'critical.value.nair.90'
epband.fun: no visible binding for global variable
  'critical.value.nair.95'
epband.fun: no visible binding for global variable
  'critical.value.nair.99'
hall.wellner.fun: no visible global function definition for 'data'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.90'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.95'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.99'
lrt.confints: no visible global function definition for 'qchisq'
rothman.fun: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/kmeRs.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'kpcalg_tutorial.Rnw' using knitr
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

Quitting from lines 61-65 (kpcalg_tutorial.Rnw) 
Error: processing vignette 'kpcalg_tutorial.Rnw' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'kpcalg_tutorial.Rnw'

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

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

> ### Name: plot
> ### Title: Plot Family of Sets
> ### Aliases: plot.kstructure plot.kbase plot.kfamset
> ### Keywords: math
> 
> ### ** Examples
> 
> fs <- kfamset(set(set("a"), set("a","b"), set("a","c"), set("d","e"), 
+    set("a","b","d","e"), set("a","c","d","e"), set("a","b","c","d","e")))
> if(require("Rgraphviz")) {plot(fs)}
Loading required package: Rgraphviz
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':

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: grid
Warning: multiple methods tables found for 'plot'
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
Error(s) in re-building vignettes:
--- re-building 'kst.Rnw' using Sweave
Loading required package: proxy

Attaching package: 'proxy'

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

    as.dist, dist

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

    as.matrix

Loading required package: relations
Loading required package: sets
Loading required namespace: Rgraphviz
Warning: multiple methods tables found for 'plot'

Error: processing vignette 'kst.Rnw' failed with diagnostics:
 chunk 11 (label = plot) 
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'

--- failed re-building 'kst.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/LANDD.Rcheck/00install.out' for details.
installed size is 79.1Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.9Mb
    proj   5.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/leapp.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
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:
+   lgr$info("More important than it seems")
+   lgr$fatal("Really not so bad")
+ })
WARN  [15:46:59.123] More important than it seems 
WARN  [15:46:59.123] Really not so bad 
> with_log_value(
+   list(msg = "overriden msg"),  {
+   lgr$info("bar")
+   lgr$fatal("FOO")
+ })
INFO  [15:46:59.123] overriden msg 
FATAL [15:46:59.123] overriden msg 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.51 0.14 5.22 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 ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/liayson.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      2.4Mb
Running 'testthat.R' [79s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > 
  > test_check("lidR")
  -- 1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalo
  projection(req2) not equal to "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clrk66 +units=m +no_defs".
  1/1 mismatches
  x[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  x[1]: k66 +units=m +no_defs "
  y[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  y[1]: k66 +units=m +no_defs"
  
  == testthat results  ===========================================================
  [ OK: 971 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalog_apply-automerge.R#171) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [85s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > 
  > test_check("lidR")
  -- 1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalo
  projection(req2) not equal to "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clrk66 +units=m +no_defs".
  1/1 mismatches
  x[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  x[1]: k66 +units=m +no_defs "
  y[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  y[1]: k66 +units=m +no_defs"
  
  == testthat results  ===========================================================
  [ OK: 971 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalog_apply-automerge.R#171) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/lmQCM.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running examples in 'loon-Ex.R' failed
The error most likely occurred in:

> ### Name: graphreduce
> ### Title: Make each space in a node apprear only once
> ### Aliases: graphreduce
> 
> ### ** Examples
> 
> G <- completegraph(nodes=LETTERS[1:4])
> LG <- linegraph(G)
> 
> LLG <- linegraph(LG)
> 
> graphreduce(LLG)
$nodes
[1] "A:B:C" "A:B:D" "A:C:D" "B:C:D"

$from
 [1] "A:B:C" "A:B:C" "A:B:C" "A:B:D" "A:B:D" "A:B:C" "A:B:D" "A:C:D" "A:C:D"
[10] "B:C:D"

$to
 [1] "A:B:D" "A:B:C" "A:C:D" "A:B:D" "A:C:D" "B:C:D" "B:C:D" "A:C:D" "B:C:D"
[10] "B:C:D"

$isDirected
[1] FALSE

attr(,"class")
[1] "loongraph"
> 
> if (requireNamespace("Rgraphviz", quietly = TRUE)) {
+   plot(graphreduce(LLG))
+ }
Warning: multiple methods tables found for 'plot'
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/LoopRig.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.1Mb
    libs   1.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.6Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
    proj   5.0Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    TS_files     5.8Mb
    base_files   6.3Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  34.2Mb
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/r-reticulate/python.exe" "d:/RCompile/CRANpkg/lib/4.0/reticulate/config/config.py"' had status 2
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/r-reticulate/python.exe" "d:/RCompile/CRANpkg/lib/4.0/reticulate/config/config.py"' had status 2

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.2Mb
    htmlwidgets   1.9Mb
    libs          6.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MazamaCoreUtils.Rcheck/00install.out' for details.
Running examples in 'MCDA-Ex.R' failed
The error most likely occurred in:

> ### Name: plotAlternativesValuesPreorder
> ### Title: Function to plot a preorder of alternatives, based on some score
> ###   or ranking.
> ### Aliases: plotAlternativesValuesPreorder
> ### Keywords: methods
> 
> ### ** Examples
> 
> library(MCDA)
> 
> alternativesValues <- c(10,1,8,3,8,3,4,4,8,5)
> 
> names(alternativesValues) <- c("x10","x1","x9","x2","x8",
+                                 "x3","x7","x4","x6","x5")
> 
> plotAlternativesValuesPreorder(alternativesValues, 
+                                 decreasing=TRUE, 
+                                 alternativesIDs=c("x10","x3","x7",
+                                                     "x4","x6","x5"))
Warning: multiple methods tables found for 'plot'
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plotAlternativesValuesPreorder ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   2.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.2Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/mcmcabn.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.5Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   5.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Mega2R.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.1Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Package suggested but not available for checking: 'unix'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/metaboGSE.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Error(s) in re-building vignettes:
--- re-building 'metan_start.Rmd' using rmarkdown
[]=====================================================[]
[] Multi-Environment Trial Analysis (metan) v1.4.0     []
[] Author: Tiago Olivoto                               []
[] Type citation('metan') to know how to cite metan    []
[] Type vignette('metan_start') for a short tutorial   []
[] Visit http://bit.ly/2TIq6JE for a complete tutorial []
[]=====================================================[]
No issues detected while inspecting data.
Quitting from lines 133-134 (metan_start.Rmd) 
Error: processing vignette 'metan_start.Rmd' failed with diagnostics:
No common type for `..1$Y` <character> and `..2$Y` <integer>.
--- failed re-building 'metan_start.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MetaPath.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'doMC', 'doSMP'
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/metap.Rcheck/00install.out' for details.
prepare_Rd: multiple methods tables found for 'plot'
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/metapro.Rcheck/00install.out' for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.7Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs   4.2Mb
    misc   1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Error(s) in re-building vignettes:
--- re-building 'MfUSampler.Rnw' using Sweave
MfUSampler 1.0.4
Convenience Functions for Multivariate MCMC Using Univariate Samplers
For citations, please use:
Alireza S. Mahani, Mansour T. A. Sharabiani (2017). Multivariate-From-Univariate MCMC Sampler: The R Package MfUSampler. Journal of Statistical Software, Code Snippets, 78(1), 1-22. doi:10.18637/jss.v078.c01

Error: processing vignette 'MfUSampler.Rnw' failed with diagnostics:
 chunk 31 
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! file33c3c5ce37d29.o:file33c3c5ce37d29.cpp:(.text+0x600): undefined reference to `dgemv_'
file33c3c5ce37d29.o:file33c3c5ce37d29.cpp:(.text+0xb2d): undefined reference to `dgemv_'
collect2.exe: error: ld returned 1 exit status

--- failed re-building 'MfUSampler.Rnw'

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

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

> ### Name: MiStatCount
> ### Title: FDR for microarray gene expression data
> ### Aliases: MiStatCount
> 
> ### ** Examples
> 
> data("IMexpression"); data("IMspecimen") # load data and specimen information
> #sampling data and specimen information
> ExpData<-MiDataSample(IMexpression, IMspecimen$diagnosis,"ebv", "norm")
> Specimens<-MiSpecimenSample(IMspecimen$diagnosis, "ebv", "norm")
> #Counting statistics
> StatRes<-MiStatCount(ExpData, Specimens)
Error: .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Execution halted
Running examples in 'MIMSunit-Ex.R' failed
The error most likely occurred in:

> ### Name: import_mhealth_csv
> ### Title: Import raw multi-channel accelerometer data stored in mHealth
> ###   Specification
> ### Aliases: import_mhealth_csv
> 
> ### ** Examples
> 
>   default_ops = options()
>   options(digits.secs=3)
>   # Use the sample mhealth csv file provided by the package
>   filepath = system.file('extdata', 'mhealth.csv', package='MIMSunit')
>   filepath
[1] "D:/temp/RtmpKqWVDo/RLIBS_199dc37d2460/MIMSunit/extdata/mhealth.csv"
> 
>   # Load the file
>   df = import_mhealth_csv(filepath)
Error: Assigned data `as.character(df[, factor_cols])` must be compatible with existing data.
x Existing data has 5000 rows.
x Assigned data has 0 rows.
i Only vectors of size 1 are recycled.
Backtrace:
    x
 1. \-MIMSunit::import_mhealth_csv(filepath)
 2.   +-base::`[<-`(`*tmp*`, , factor_cols, value = character(0))
 3.   \-tibble:::`[<-.tbl_df`(`*tmp*`, , factor_cols, value = character(0))
 4.     \-tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       \-tibble:::vectbl_recycle_rhs(...)
 6.         \-base::tryCatch(...)
 7.           \-base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               \-value[[3L]](cond)
Execution halted
cdf.pval: no visible global function definition for 'median'
cdf.pval: no visible binding for global variable 'ecdf'
find_hits: no visible global function definition for 'na.omit'
mad.scores: no visible global function definition for 'as.formula'
mad.scores: no visible binding for global variable 'median'
mad.scores: no visible binding for global variable 'mad'
rm.outliers: no visible global function definition for 'as.formula'
rm.outliers: no visible binding for global variable 'median'
rm.outliers: no visible binding for global variable 'mad'
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/miRtest.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mixKernel.Rcheck/00install.out' for details.
listGenoToTable: no visible binding for global variable 'dummy'
Undefined global functions or variables:
  dummy
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MM2S.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'MoBPSmaps'
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc  23.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MomTrunc.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   9.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   1.4Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    libs         13.9Mb
    mathematica   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MRPC.Rcheck/00install.out' for details.
File 'MRwarping/libs/i386/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'
File 'MRwarping/libs/x64/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running examples in 'MSbox-Ex.R' failed
The error most likely occurred in:

> ### Name: describe
> ### Title: Get the compound information
> ### Aliases: describe
> 
> ### ** Examples
> 
> describe('malic acid', "formula")
Warning in open.connection(x, "rb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in open.connection(x, "rb") : cannot open the connection
Calls: describe ... read_xml.character -> read_xml.connection -> open -> open.connection
Execution halted
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  20.9Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MSIseq.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/msSurv.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/multicross.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Error(s) in re-building vignettes:
--- re-building 'TwoModeNetworks.Rnw' using knitr
Quitting from lines 128-132 (TwoModeNetworks.Rnw) 
Error: processing vignette 'TwoModeNetworks.Rnw' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'TwoModeNetworks.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/mutossGUI.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/mutoss.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
    libs   1.5Mb
Running examples in 'nandb-Ex.R' failed
The error most likely occurred in:

> ### Name: brightness
> ### Title: Calculate brightness from image series.
> ### Aliases: brightness
> 
> ### ** Examples
> 
> img <- ijtiff::read_tif(system.file("extdata", "50.tif", package = "nandb"))
Error:  The function `ijtiff::read_tif()` is not available on 32-bit windows machines. 
    * 64-bit windows and any Linux or Mac will work.
    * I am sorry about this, I spent many hours trying to get it to work on 32-bit Windows machines but I failed.
Backtrace:
    x
 1. \-ijtiff::read_tif(system.file("extdata", "50.tif", package = "nandb"))
 2.   \-ijtiff:::err_on_win32bit("read_tif")
 3.     \-ijtiff:::custom_stop(...)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'exploring-imputed-values.Rmd' using rmarkdown
Quitting from lines 78-87 (exploring-imputed-values.Rmd) 
Error: processing vignette 'exploring-imputed-values.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building 'exploring-imputed-values.Rmd'

--- re-building 'getting-started-w-naniar.Rmd' using rmarkdown
Quitting from lines 284-292 (getting-started-w-naniar.Rmd) 
Error: processing vignette 'getting-started-w-naniar.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building 'getting-started-w-naniar.Rmd'

--- re-building 'naniar-visualisation.Rmd' using rmarkdown
--- finished re-building 'naniar-visualisation.Rmd'

--- re-building 'replace-with-na.Rmd' using rmarkdown
Quitting from lines 43-52 (replace-with-na.Rmd) 
Error: processing vignette 'replace-with-na.Rmd' failed with diagnostics:
No common type for `y` <character> and `y` <double>.
--- failed re-building 'replace-with-na.Rmd'

--- re-building 'special-missing-values.Rmd' using rmarkdown
--- finished re-building 'special-missing-values.Rmd'

SUMMARY: processing the following files failed:
  'exploring-imputed-values.Rmd' 'getting-started-w-naniar.Rmd'
  'replace-with-na.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.9Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
File 'NeatMap/libs/i386/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'
File 'NeatMap/libs/x64/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/netgsa.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    CppCode   2.6Mb
    R         6.1Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/NIPTeR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/nlcv.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs   2.7Mb
File 'nws/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for 'flush.console'
nwsPkgInfo: no visible global function definition for
  'packageDescription'
initialize,nwsServer: no visible global function definition for
  'make.socket'
initialize,nwsServer: no visible global function definition for
  'close.socket'
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
File 'obliclus/libs/i386/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'
File 'obliclus/libs/x64/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.3Mb
    help   2.7Mb
    libs   2.0Mb
mapvar: no visible global function definition for 'data'
mapvar: no visible binding for global variable 'state.fips'
mapvar: no visible global function definition for 'rgb'
mapvar: no visible global function definition for 'rect'
mapvar: no visible global function definition for 'text'
rowScrape: no visible global function definition for 'tail'
rowScrape: no visible global function definition for 'head'
scrapeTable: no visible binding for global variable 'tail'
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/omu.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
MLparameters: no visible global function definition for 'optim'
comp.freq: no visible global function definition for 'x11'
comp.freq: no visible global function definition for 'par'
Undefined global functions or variables:
  optim par x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par")
  importFrom("stats", "optim")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/ontologyPlot.Rcheck/00install.out' for details.
Running examples in 'ontologyPlot-Ex.R' failed
The error most likely occurred in:

> ### Name: onto_plot
> ### Title: Get 'ontology_plot' object
> ### Aliases: onto_plot
> 
> ### ** Examples
> 
> library(ontologyIndex)
> data(hpo)
> hpo_phenotypes <- c(
+ 	A=c("HP:0001382","HP:0004272","HP:0007917","HP:0004912","HP:0001596"),
+ 	B=c("HP:0001382","HP:0004272","HP:0002165","HP:0004800","HP:0004912"),
+ 	C=c("HP:0004800","HP:0001382","HP:0004912","HP:0007917","HP:0008743"),
+ 	D=c("HP:0001257","HP:0001382","HP:0007917","HP:0012623","HP:0002165"),
+ 	E=c("HP:0007917","HP:0004800","HP:0004272","HP:0001596","HP:0002165")
+ )
> 
> onto_plot(
+ 	ontology=hpo,
+ 	term_sets=hpo_phenotypes
+ )
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: <Anonymous> ... plot.ontology_plot -> plot -> plot -> plot.default -> xy.coords
Execution halted
Error(s) in re-building vignettes:
--- re-building 'plotting-ontological-terms.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 31-32 (plotting-ontological-terms.Rmd) 
Error: processing vignette 'plotting-ontological-terms.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'plotting-ontological-terms.Rmd'

--- re-building 'plotting-term-grids.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'plotting-term-grids.Rmd'

SUMMARY: processing the following file failed:
  'plotting-ontological-terms.Rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/OpenCL.Rcheck/00install.out' for details.
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    libs   20.0Mb
    share   9.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
Running 'testthat.R' [23s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(OpenLand)
  > 
  > test_check("OpenLand")
  -- 1. Error: (unknown) (@test_generalfunctions.R#29)  --------------------------
  package 'rgdal' is not available
  Backtrace:
    1. base::lapply(...)
    2. OpenLand:::FUN(X[[i]], ...)
    4. raster::writeRaster(...)
    5. raster:::.local(x, filename, ...)
    6. raster:::.writeGDALall(...)
    7. raster:::.startGDALwriting(...)
    8. raster:::.getGDALtransient(...)
    9. raster:::.isSupportedFormat(gdalfiletype)
   10. raster:::.isSupportedGDALFormat(dname)
   11. raster:::.requireRgdal()
  
  -- 2. Error: (unknown) (@test_inputrasters.R#5)  -------------------------------
  package 'rgdal' is not available
  Backtrace:
    1. base::lapply(...)
    2. OpenLand:::FUN(X[[i]], ...)
    4. raster::writeRaster(...)
    5. raster:::.local(x, filename, ...)
    6. raster:::.writeGDALall(...)
    7. raster:::.startGDALwriting(...)
    8. raster:::.getGDALtransient(...)
    9. raster:::.isSupportedFormat(gdalfiletype)
   10. raster:::.isSupportedGDALFormat(dname)
   11. raster:::.requireRgdal()
  
  == testthat results  ===========================================================
  [ OK: 96 | SKIPPED: 0 | WARNINGS: 24 | FAILED: 2 ]
  1. Error: (unknown) (@test_generalfunctions.R#29) 
  2. Error: (unknown) (@test_inputrasters.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.6Mb
    models   4.6Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.6Mb
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File 'OriGen/libs/i386/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'
File 'OriGen/libs/x64/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/orQA.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Package suggested but not available for checking: 'Rcplex'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/PAMA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/PANDA.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.2Mb
    doc    2.1Mb
Running examples in 'pathfindR-Ex.R' failed
The error most likely occurred in:

> ### Name: input_processing
> ### Title: Process Input
> ### Aliases: input_processing
> 
> ### ** Examples
> 
> ## Don't show: 
> input_processing(RA_input[1:20, ], 0.05, "KEGG")
Number of genes provided in input: 20
Number of genes in input after p-value filtering: 20
Error: .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Execution halted
Error(s) in re-building vignettes:
--- re-building 'intro_vignette.Rmd' using rmarkdown
--- finished re-building 'intro_vignette.Rmd'

--- re-building 'manual_execution.Rmd' using rmarkdown
Quitting from lines 45-49 (manual_execution.Rmd) 
Error: processing vignette 'manual_execution.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
--- failed re-building 'manual_execution.Rmd'

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

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

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

> ### Name: probeMerge
> ### Title: Function to merge probesets
> ### Aliases: probeMerge probeMerge,micro_array-method
> ### Keywords: manip
> 
> ### ** Examples
> 
> if(require(CascadeData)){
+ data(micro_S)
+ D<-as.micro_array(micro_S[1:2000,],1:4,6)
+ D@gene_ID<-jetset::scores.hgu133plus2[D@name,"EntrezID"]
+ PM <- probeMerge(D)
+ }
Loading required package: CascadeData
Error: .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Execution halted
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
get.sysenv: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   4.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      1.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  13.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/PCGSE.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/PCS.Rcheck/00install.out' for details.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs   13.3Mb
    share  11.9Mb
Running 'script.R' [1s]
  Running 'testthat.R' [3s]
Running the tests in 'tests/script.R' failed.
Complete output:
  > ## I initially tried writing these tests using testthat, but I got
  > ## errors when using the system() and system2() functions (bug in
  > ## testthat).
  > PeakError_compute.R <- system.file(
  +   "exampleData", "PeakError_compute.R",
  +   mustWork=TRUE,
  +   package="PeakError")
  > Rscript <- R.home(file.path("bin", "Rscript"))
  > exampleData <- system.file("exampleData", package="PeakError", mustWork=TRUE)
  > peaks.bed <- file.path(exampleData, "peaks.bed")
  > labels.bed <- file.path(exampleData, "labels.bed")
  > overlapping.bed <- file.path(exampleData, "overlapping_peaks.bed")
  > 
  > ##test_that("PeakError_compute.R correct", {
  > out.file <- tempfile()
  > cmd <- paste(Rscript, PeakError_compute.R, peaks.bed, labels.bed, ">", out.file)
  > status <- system(cmd)
  Error: Usage: compute_error.R peaks.bed labels.bed > errors.bed
  Execution halted
  > errors <- read.table(out.file, sep="\t", header=TRUE)
  Error in file(file, "rt") : cannot open the connection
  Calls: read.table -> file
  In addition: Warning message:
  In file(file, "rt") :
    cannot open file 'D:\temp\Rtmp0e73BX\file2270774278ae': No such file or directory
  Execution halted
Running 'script.R' [1s]
  Running 'testthat.R' [2s]
Running the tests in 'tests/script.R' failed.
Complete output:
  > ## I initially tried writing these tests using testthat, but I got
  > ## errors when using the system() and system2() functions (bug in
  > ## testthat).
  > PeakError_compute.R <- system.file(
  +   "exampleData", "PeakError_compute.R",
  +   mustWork=TRUE,
  +   package="PeakError")
  > Rscript <- R.home(file.path("bin", "Rscript"))
  > exampleData <- system.file("exampleData", package="PeakError", mustWork=TRUE)
  > peaks.bed <- file.path(exampleData, "peaks.bed")
  > labels.bed <- file.path(exampleData, "labels.bed")
  > overlapping.bed <- file.path(exampleData, "overlapping_peaks.bed")
  > 
  > ##test_that("PeakError_compute.R correct", {
  > out.file <- tempfile()
  > cmd <- paste(Rscript, PeakError_compute.R, peaks.bed, labels.bed, ">", out.file)
  > status <- system(cmd)
  Error: Usage: compute_error.R peaks.bed labels.bed > errors.bed
  Execution halted
  > errors <- read.table(out.file, sep="\t", header=TRUE)
  Error in file(file, "rt") : cannot open the connection
  Calls: read.table -> file
  In addition: Warning message:
  In file(file, "rt") :
    cannot open file 'D:\temp\RtmpSUnURi\filedfc439a376cb': No such file or directory
  Execution halted
Malformed Title field: should not end in a period.
'LinkingTo' for 'ggplot2' is unused as it has no 'include' directory
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:11255 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11255 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/phateR.Rcheck/00install.out' for details.
Running examples in 'phenocamapi-Ex.R' failed
The error most likely occurred in:

> ### Name: download_midday_images
> ### Title: Downloading the midday images for PhenoCam sites given a time
> ###   range
> ### Aliases: download_midday_images
> 
> ### ** Examples
> 
> 
> download_dir <- download_midday_images('dukehw',
+  y = 2018,
+  months = 2,
+  days=1,
+  download_dir= tempdir())
Warning in get_midday_list(site, direct = FALSE) :
  midday list file was not found on the Phenocam server!
Error in basename(filepaths) : a character vector argument expected
Calls: download_midday_images -> parse_phenocam_filenames -> gsub -> basename
Execution halted
Running 'testthat.R' [44s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Content type 'application/octet-stream' length 206183 bytes (201 KB)
  ==================================================
  downloaded 201 KB
  
  -- 1. Failure: test getting awb data (@testphenocamapi.R#42)  ------------------
  `wb` not equal to "LIKELY_NO".
  target is NULL, current is character
  
  == testthat results  ===========================================================
  [ OK: 5 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: test getting awb data (@testphenocamapi.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_phenocam_api.Rmd' using rmarkdown
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 206183 bytes (201 KB)
==================================================
downloaded 201 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/2013/05/dukehw_2013_05_31_150331.jpg'
Content type 'image/jpeg' length 470270 bytes (459 KB)
==================================================
downloaded 459 KB

Quitting from lines 282-298 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
a character vector argument expected
--- failed re-building 'getting_started_phenocam_api.Rmd'

--- re-building 'phenocam_data_fusion.Rmd' using rmarkdown
Loading required package: rjson
Loading required package: RCurl
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 206183 bytes (201 KB)
==================================================
downloaded 201 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/oregonMP/ROI/oregonMP_EN_1000_3day.csv'
Content type 'application/octet-stream' length 272237 bytes (265 KB)
==================================================
downloaded 265 KB

--- finished re-building 'phenocam_data_fusion.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.0Mb
    libs      1.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/phyloseqGraphTest.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.8Mb
Running 'test-async.R' [18s]
  Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pkgcache)
  > 
  > test_check("pkgcache")
  -- 1. Error: load_primary_pkgs (@test-metadata-cache.R#191)  -------------------
  No metadata available
  Backtrace:
   1. pkgcache:::synchronise(get_private(cmc)$load_primary_pkgs(oneday()))
   2. get_private(cmc)$load_primary_pkgs(oneday())
   3. pkgcache:::cmc__load_primary_pkgs(self, private, max_age)
   4. private$update_replica_rds(alert = FALSE)
   5. pkgcache:::cmc__update_replica_rds(self, private, alert)
  
  == testthat results  ===========================================================
  [ OK: 305 | SKIPPED: 28 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: load_primary_pkgs (@test-metadata-cache.R#191) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/PlasmaMutationDetector.Rcheck/00install.out' for details.
Running examples in 'plot3logit-Ex.R' failed
The error most likely occurred in:

> ### Name: field3logit
> ### Title: Computation of the vector field
> ### Aliases: field3logit plot3logit print.field3logit plot.field3logit
> ###   as.data.frame.field3logit fortify.field3logit
> 
> ### ** Examples
> 
> data(cross_1year)
> 
> # Model fit
> mod0 <- nnet::multinom(employment_sit ~ finalgrade + irregularity + hsscore,
+   cross_1year)
# weights:  21 (12 variable)
initial  value 3605.645531 
iter  10 value 2187.709284
iter  20 value 2157.087955
final  value 2157.087854 
converged
> mod0
Call:
nnet::multinom(formula = employment_sit ~ finalgrade + irregularity + 
    hsscore, data = cross_1year)

Coefficients:
           (Intercept) finalgradeLow finalgradeHigh irregularityLow
Unemployed  -0.4481761    0.05551765    -0.07810893     -0.01874354
Trainee     -1.3751140    0.14456683    -0.26849829      0.05764144
           irregularityHigh      hsscore
Unemployed       0.15691595 -0.016619227
Trainee         -0.03477569 -0.009964381

Residual Deviance: 4314.176 
AIC: 4338.176 
> 
> # Assessing the effect of "finalgradeHigh" (explicit notation)
> field0 <- field3logit(mod0, c(0, 0, 1, 0, 0, 0))
> gg3logit(field0) + stat_3logit()
Error: $ operator is invalid for atomic vectors
Execution halted
Error(s) in re-building vignettes:
--- re-building 'plot3logit-overview.Rmd' using rmarkdown
Loading required package: ggtern
Loading required package: ggplot2
--
Remember to cite, run citation(package = 'ggtern') for further info.
--

Attaching package: 'ggtern'

The following objects are masked from 'package:ggplot2':

    %+%, aes, annotate, calc_element, ggplot, ggplotGrob, ggplot_build,
    ggplot_gtable, ggsave, layer_data, theme, theme_bw, theme_classic,
    theme_dark, theme_gray, theme_light, theme_linedraw, theme_minimal,
    theme_void

Loading required package: Ternary
Quitting from lines 95-96 (plot3logit-overview.Rmd) 
Error: processing vignette 'plot3logit-overview.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building 'plot3logit-overview.Rmd'

SUMMARY: processing the following file failed:
  'plot3logit-overview.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Found the following significant warnings:
  Warning: `data_frame()` is deprecated as of tibble 1.1.0.
See 'd:/Rcompile/CRANpkg/local/4.0/poio.Rcheck/00install.out' for details.
Running examples in 'polyCub-Ex.R' failed
The error most likely occurred in:

> ### Name: polyCub.exact.Gauss
> ### Title: Quasi-Exact Cubature of the Bivariate Normal Density
> ### Aliases: polyCub.exact.Gauss
> ### Keywords: math spatial
> 
> ### ** Examples
> 
> ## a function to integrate (here: isotropic zero-mean Gaussian density)
> f <- function (s, sigma = 5)
+     exp(-rowSums(s^2)/2/sigma^2) / (2*pi*sigma^2)
> 
> ## a simple polygon as integration domain
> hexagon <- list(
+     list(x = c(7.33, 7.33, 3, -1.33, -1.33, 3),
+          y = c(-0.5, 4.5, 7, 4.5, -0.5, -3))
+ )
> 
> ## quasi-exact integration based on gpclib::tristrip() and mvtnorm::pmvnorm()
> if (requireNamespace("mvtnorm") && gpclibPermit()) {
+     hexagon.gpc <- new("gpc.poly", pts = lapply(hexagon, c, list(hole = FALSE)))
+     plotpolyf(hexagon.gpc, f, xlim = c(-8,8), ylim = c(-8,8))
+     print(polyCub.exact.Gauss(hexagon.gpc, mean = c(0,0), Sigma = 5^2*diag(2),
+                               plot = TRUE), digits = 16)
+ }
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: print ... polyCub.exact.Gauss -> plot -> plot -> plot.default -> xy.coords
Execution halted
Error(s) in re-building vignettes:
--- re-building 'polyRADtutorial.Rmd' using rmarkdown

For example usage please run: vignette('qqman')

Citation appreciated but not required:
Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv DOI: 10.1101/005165 (2014).

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

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
Error: package or namespace load failed for 'S4Vectors':
 .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Quitting from lines 410-413 (polyRADtutorial.Rmd) 
Error: processing vignette 'polyRADtutorial.Rmd' failed with diagnostics:
package 'S4Vectors' could not be loaded
--- failed re-building 'polyRADtutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0/PPRL.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'preputils.Rmd' using rmarkdown
Error: processing vignette 'preputils.Rmd' failed with diagnostics:
Scanner error: while parsing a quoted scalar at line 3, column 7 found unknown escape character at line 10, column 4

--- failed re-building 'preputils.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/pRF.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/prioGene.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ProbeDeveloper.Rcheck/00install.out' for details.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      1.6Mb
Running 'run-all.R' [33s]
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("ProjectTemplate")
  Loading required package: ProjectTemplate
  -- 1. Failure: Custom configuration is added to config (@test-add_config.R#12)  
  `load.project()` generated warnings:
  * 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
  
  v |  OK F W S | Context
  
  / |   0       | Example tests
  v |   1       | Example tests
  
  == Results =====================================================================
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  v |  OK F W S | Context
  
  / |   0       | Example tests
  v |   1       | Example tests
  
  == Results =====================================================================
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] TRUE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  == testthat results  ===========================================================
  [ OK: 852 | SKIPPED: 4 | WARNINGS: 281 | FAILED: 1 ]
  1. Failure: Custom configuration is added to config (@test-add_config.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
    proj   5.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   1.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    libs   1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/psSubpathway.Rcheck/00install.out' for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/pulseTD.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Error(s) in re-building vignettes:
--- re-building 'qtlnet.Rnw' using Sweave
Loading required package: qtl
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: sem
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:igraph':

    normalize, path, union

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


Attaching package: 'graph'

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

    degree, edges, intersection

Loading required package: pcalg

Error: processing vignette 'qtlnet.Rnw' failed with diagnostics:
 chunk 2 
Error in igraph::graph.data.frame(edges, TRUE, vertices = vertices) : 
  Some vertex names in edge list are not listed in vertex data frame

--- failed re-building 'qtlnet.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   2.5Mb
Error(s) in re-building vignettes:
--- re-building 'quickstart.Rmd' using rmarkdown
Package version: 2.0.1
Parallel computing: 2 of 32 threads used.
See https://quanteda.io for tutorials and examples.

Attaching package: 'quanteda'

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

    View

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-14'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 381-396 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'quickstart.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
File 'qVarSel/libs/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   1.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/rags2ridges.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/ragt2ridges.Rcheck/00install.out' for details.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   6.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   3.0Mb
.disableThreads: no visible global function definition for
  'stopCluster'
.enableThreads: no visible global function definition for 'detectCores'
.enableThreads: no visible global function definition for
  'makePSOCKcluster'
.enableThreads: no visible global function definition for
  'clusterExport'
.enableThreads: no visible global function definition for 'clusterCall'
.forwardSelection: no visible binding for global variable 'var'
.forwardSelection: no visible global function definition for 'glm'
.forwardSelection: no visible global function definition for 'formula'
.forwardSelection: no visible global function definition for 'binomial'
.forwardSelection: no visible global function definition for 'lm'
.forwardSelection: no visible global function definition for 'predict'
.predict.internal: no visible global function definition for 'predict'
randomGLM: no visible binding for global variable 'cor'
randomGLM: no visible binding for global variable 'sd'
randomGLM: no visible global function definition for 'var'
thinRandomGLM: no visible global function definition for 'glm'
thinRandomGLM: no visible global function definition for 'binomial'
thinRandomGLM: no visible global function definition for 'lm'
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/randstr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RAPIDR.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   2.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.8Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0/Rblpapi.Rcheck/00install.out' for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    cont  25.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RcmdrPlugin.BiclustGUI.Rcheck/00install.out' for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/Rcplex.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    include   6.2Mb
    libs      1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       3.9Mb
    libs      2.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.8Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       8.9Mb
    libs      1.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rcpp.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
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 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
Error(s) in re-building vignettes:
--- re-building 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' using rmarkdown
Loading required package: rJava
Loading required package: Rdroolsjars

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: 'purrr'

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Quitting from lines 183-187 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
Assigned data `paste(seq(as.numeric(lowerRange), as.numeric(upperRange)), collapse = ",")` must be compatible with existing data.
i Error occurred for column `Indices`.
x No common type for `value` <character> and `x` <double>.
--- failed re-building 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'readabs_vignette.Rmd' using rmarkdown
Quitting from lines 64-67 (readabs_vignette.Rmd) 
Error: processing vignette 'readabs_vignette.Rmd' failed with diagnostics:
cannot open URL 'https://ausstats.abs.gov.au/servlet/TSSearchServlet?catno=6345.0&pg=1'
--- failed re-building 'readabs_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(readroper)
  readroper package loaded.
  > 
  > test_check("readroper")
  -- 1. Error: First row of multicard dataset matches (@test-readroper.R#4)  -----
  Must subset rows with a valid subscript vector.
  i Logical subscripts must match the size of the indexed input.
  x The input has size 1976 but the subscript `card_v` has size 2.
  Backtrace:
    1. readroper::read_rpr(...)
   16. vctrs:::stop_indicator_size(...)
  
  == testthat results  ===========================================================
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: First row of multicard dataset matches (@test-readroper.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for 'abline'
bestmods: no visible global function definition for 'axis'
bestmods: no visible global function definition for 'lines'
cic: no visible global function definition for 'lsfit'
cic: no visible global function definition for 'var'
cvic: no visible global function definition for 'lsfit'
cvic: no visible global function definition for 'lm'
eic: no visible global function definition for 'lsfit'
eic: no visible global function definition for 'lm'
ic.min: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'var'
xy: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.7Mb
Running 'test-all.R' [7s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > # Modeled after the R6 testing structure: https://github.com/wch/R6/blob/master/tests/testthat.R
  > library(testthat)
  > library(REDCapR)
  > 
  > testthat::test_check("REDCapR")
  -- 1. Failure: validate_no_logical -concern dataset (@test-validate.R#36)  -----
  ds$field_index not equal to 2.
  names for target but not for current
  
  == testthat results  ===========================================================
  [ OK: 135 | SKIPPED: 79 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: validate_no_logical -concern dataset (@test-validate.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package which this enhances but not available for checking: 'Rcplex'
Error(s) in re-building vignettes:
--- re-building 'relations.Rnw' using Sweave
Loading required package: Rgraphviz
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':

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: grid
Warning: multiple methods tables found for 'plot'

Error: processing vignette 'relations.Rnw' failed with diagnostics:
 chunk 8 (label = plot) 
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'

--- failed re-building 'relations.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Running examples in 'rematch2-Ex.R' failed
The error most likely occurred in:

> ### Name: re_exec
> ### Title: Extract Data From First Regular Expression Match Into a Data
> ###   Frame
> ### Aliases: re_exec $.rematch_records $.rematch_allrecords
> 
> ### ** Examples
> 
> name_rex <- paste0(
+   "(?<first>[[:upper:]][[:lower:]]+) ",
+   "(?<last>[[:upper:]][[:lower:]]+)"
+ )
> notables <- c(
+   "  Ben Franklin and Jefferson Davis",
+   "\tMillard Fillmore"
+ )
> # Match first occurrence
> pos <- re_exec(notables, name_rex)
> pos
Error: Input must be a vector, not a `rematch_records` object.
Backtrace:
     x
  1. +-(function (x, ...) ...
  2. +-tibble:::print.tbl(x)
  3. | +-cli::cat_line(format(x, ..., n = n, width = width, n_extra = n_extra))
  4. | | \-base::paste0(..., collapse = "\n")
  5. | +-base::format(x, ..., n = n, width = width, n_extra = n_extra)
  6. | \-tibble:::format.tbl(x, ..., n = n, width = width, n_extra = n_extra)
  7. |   \-tibble::trunc_mat(x, n = n, width = width, n_extra = n_extra)
  8. |     +-base::as.data.frame(head(x, n))
  9. |     +-utils::head(x, n)
 10. |     \-utils:::head.data.frame(x, n)
 11. |       +-base::do.call("[", args)
 12. |       +-x[1:2, , drop = FALSE]
 13. |       \-tibble:::`[.tbl_df`(x, 1:2, , drop = FALSE)
 14. |         \-tibble:::tbl_subset_row(xo, i = i, i_arg)
 15. |           \-base::lapply(unclass(x), vec_slice, i = i)
 16. |             \-vctrs:::FUN(X[[i]], ...)
 17. \-vctrs:::stop_scalar_type(...)
 18.   \-vctrs:::stop_vctrs(msg, "vctrs_error_scala
Execution halted
Running examples in 'rEMM-Ex.R' failed
The error most likely occurred in:

> ### Name: combine
> ### Title: Combining EMM Objects
> ### Aliases: c c,EMM-method
> ### Keywords: manip
> 
> ### ** Examples
> 
> data("16S")
> 
> ## create two EMMs for different data
> emm1 <- EMM("Kullback", threshold=0.1, data=Mollicutes16S+1)
> emm2 <- EMM("Kullback", threshold=0.1, data=Alphaproteobacteria16S+1)
> 
> ## combine the two EMMs
> emm12 <- c(emm1, emm2)
> ## this is the same as:
> ## emm12 <- copy(emm1)
> ## c(emm12, emm2, copy=FALSE)
> 
> ## recluster states so similar states in the to EMMs will be merged
> emm12r <- recluster_tNN(emm12)
> 
> op <- par(mfrow = c(1, 2), pty = "s")
> plot(emm12, method="graph", main="Two EMMs")
Warning: multiple methods tables found for 'plot'
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
Error(s) in re-building vignettes:
--- re-building 'rEMM.Rnw' using Sweave
Loading required package: proxy

Attaching package: 'proxy'

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

    as.dist, dist

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

    as.matrix

Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union


Attaching package: 'rEMM'

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

    as.igraph, clusters

Warning: multiple methods tables found for 'plot'

Error: processing vignette 'rEMM.Rnw' failed with diagnostics:
 chunk 6 (label = Traffic_graph) 
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'

--- failed re-building 'rEMM.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.7Mb
CA: no visible global function definition for 'readClipboard'
LL: no visible global function definition for 'readClipboard'
US: no visible global function definition for 'readClipboard'
delete: no visible global function definition for 'menu'
doc_temp: no visible global function definition for 'menu'
html5: no visible global function definition for 'na.omit'
install_pandoc: no visible global function definition for
  'download.file'
latexlist: no visible global function definition for 'readClipboard'
new_report: no visible global function definition for 'tail'
new_report: no visible global function definition for 'head'
new_report: no visible global function definition for 'menu'
presentation: no visible global function definition for 'head'
presentation: no visible global function definition for 'tail'
presentation: no visible global function definition for 'menu'
repo2github: no visible global function definition for 'download.file'
repo2github: no visible global function definition for 'unzip'
reveal.js: no visible global function definition for 'na.omit'
strWrap: no visible global function definition for 'readClipboard'
update_bib: no visible global function definition for 'tail'
update_bib: no visible global function definition for 'menu'
Undefined global functions or variables:
  download.file head menu na.omit readClipboard tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "readClipboard",
             "tail", "unzip")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/restfulr.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Error(s) in re-building vignettes:
--- re-building 'RFmerge-RainfallExample-minimal.Rmd' using rmarkdown

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Loading required package: sp
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: D:/temp/RtmpUX5erV/RLIBS_2e18073c92626/rgdal/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: D:/temp/RtmpUX5erV/RLIBS_2e18073c92626/rgdal/proj
 Linking to sp version: 1.4-1 
(C) 2019 M. Zambrano-Bigiarini and Oscar M. Baez-Villanueva (GPL >=3 license)
Type 'citation('RFmerge')' to see how to cite this package
Quitting from lines 268-274 (RFmerge-RainfallExample-minimal.Rmd) 
Error: processing vignette 'RFmerge-RainfallExample-minimal.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'RFmerge-RainfallExample-minimal.Rmd'

SUMMARY: processing the following file failed:
  'RFmerge-RainfallExample-minimal.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RGCxGC.Rcheck/00install.out' for details.
installed size is 80.3Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   2.8Mb
    libs      6.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.7Mb
Found a 'configure.in' file: 'configure.ac' has long been preferred.
prepare_Rd: replacing previous import 'sf::st_make_valid' by 'lwgeom::st_make_valid' when loading 'tmap'
Running examples in 'RGISTools-Ex.R' failed
The error most likely occurred in:

> ### Name: varEVI
> ### Title: Calculate the enhanced vegetation index (EVI)
> ### Aliases: varEVI
> 
> ### ** Examples
> 
> # path to the cropped and cutted MODIS images for the region of Navarre
> wdir <- system.file("ExNavarreVar", package = "RGISTools")
> # list all the tif files
> files.mod <- list.files(wdir, pattern = "\\.tif$", recursive = TRUE, full.names = TRUE)
> # print the MOD09 bands
> getRGISToolsOpt("MOD09BANDS")
           red            nir           blue          green          tirs1 
       "B01_1"        "B02_1"        "B03_1"        "B04_1"        "B05_1" 
         swir1          swir2        quality          cloud 
       "B06_1"        "B07_1" "_state_1km_1"          "CLD" 
> scale.factor <- 0.0001
> 
> # select the red, blue and nir bands
> img.mod.red <- raster(files.mod[1]) * scale.factor
Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",  : 
  Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Calls: raster -> raster -> .local -> .rasterObjectFromFile
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.5Mb
    libs    2.1Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.7Mb
    libs   5.0Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.2Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/RichR.Rcheck/00install.out' for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    lib    3.8Mb
    libs   4.9Mb
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(riskclustr)
  > 
  > test_check("riskclustr")
  -- 1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_message(...)
    6. riskclustr::optimal_kmeans_d(...)
    7. base::lapply(...)
    8. riskclustr:::FUN(X[[i]], ...)
    9. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   12. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   13. tibble:::tbl_subset_row(xo, i = i, i_arg)
   14. tibble:::vectbl_as_row_index(i, x, i_arg)
   15. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   22. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  -- 2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_equal(...)
    4. riskclustr::optimal_kmeans_d(...)
    5. base::lapply(...)
    6. riskclustr:::FUN(X[[i]], ...)
    7. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   10. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   11. tibble:::tbl_subset_row(xo, i = i, i_arg)
   12. tibble:::vectbl_as_row_index(i, x, i_arg)
   13. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   20. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  == testthat results  ===========================================================
  [ OK: 26 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_kmeans_d.R#49) 
  2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_kmeans_d.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'calculate_d.Rmd' using rmarkdown
--- finished re-building 'calculate_d.Rmd'

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

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building 'factor_pvalue.Rmd'

--- re-building 'optimal_d.Rmd' using rmarkdown
Quitting from lines 36-46 (optimal_d.Rmd) 
Error: processing vignette 'optimal_d.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building 'optimal_d.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RMaCzek.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rmagic.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Running examples in 'RmarineHeatWaves-Ex.R' failed
The error most likely occurred in:

> ### Name: detect
> ### Title: Detect heatwaves and cold-spells.
> ### Aliases: detect
> 
> ### ** Examples
> 
> ts_dat <- make_whole(sst_WA)
> res <- detect(ts_dat, climatology_start = "1983-01-01",
+               climatology_end = "2012-12-31")
Error: Assigned data `zoo::na.approx(tDat[59:61, no_NA], maxgap = 1, na.rm = TRUE)` must be compatible with existing data.
i Error occurred for column `doy`.
x Can't cast <double[,31]> to <double>.
Can not decrease dimensions.
Backtrace:
    x
 1. \-RmarineHeatWaves::detect(...)
 2.   +-base::`[<-`(...)
 3.   \-tibble:::`[<-.tbl_df`(...)
 4.     \-tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       \-tibble:::tbl_subassign_row(xj, i, value, value_arg)
 6.         \-base::tryCatch(...)
 7.           \-base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               \-value[[3L]](cond)
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rminer.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rmRNAseq.Rcheck/00install.out' for details.
Running examples in 'rmutil-Ex.R' failed
The error most likely occurred in:

> ### Name: tvctomat
> ### Title: Create a Time-varying, Intra-individual Covariate (tvcov) Object
> ### Aliases: tvctomat
> ### Keywords: manip
> 
> ### ** Examples
> 
> z <- matrix(rpois(20,5),ncol=5)
> print(tvc <- tvctomat(z, units="days"))
           
Names: z   
Units: days
Number of individuals:                4 
Number of observations:               20 
Number of observations per individual:
 5 5 5 5 
> covariates(tvc)
 [1]  4  3  6  6  6  4  8  2  4 11  5  9  3  7  4  8  6  3  5  7
> names(tvc)
[1] "z"
> v <- data.frame(matrix(rep(c("a","b","c","d","e"),4),ncol=5))
> print(tvc2 <- tvctomat(v, oldtvc=tvc, units=NA))
                
Names: z    v   
Units: days <NA>
Number of individuals:                4 
Number of observations:               20 
Number of observations per individual:
 5 5 5 5 
> covariates(tvc2)
    z v
1   4 a
2   3 e
3   6 d
4   6 c
5   6 b
6   4 b
7   8 a
8   2 e
9   4 d
10 11 c
11  5 c
12  9 b
13  3 a
14  7 e
15  4 d
16  8 d
17  6 c
18  3 b
19  5 a
20  7 e
> print(tvc3 <- tvctomat(v, oldtvc=tvc, dataframe=FALSE, units=NA))
                               
Names: z    vb   vc   vd   ve  
Units: days <NA> <NA> <NA> <NA>
Number of individuals:                4 
Number of observations:               20 
Number of observations per individual:
 5 5 5 5 
> covariates(tvc3)
    z vb vc vd ve
1   4  0  0  0  0
2   3  0  0  0  1
3   6  0  0  1  0
4   6  0  1  0  0
5   6  1  0  0  0
6   4  1  0  0  0
7   8  0  0  0  0
8   2  0  0  0  1
9   4  0  0  1  0
10 11  0  1  0  0
11  5  0  1  0  0
12  9  1  0  0  0
13  3  0  0  0  0
14  7  0  0  0  1
15  4  0  0  1  0
16  8  0  0  1  0
17  6  0  1  0  0
18  3  1  0  0  0
19  5  0  0  0  0
20  7  0  0  0  1
> print(tvc4 <- tvctomat(tvc2, interaction=c("z","v")))
Error in dimnames(x) <- dn : 
  length of 'dimnames' [2] not equal to array extent
Calls: print -> tvctomat -> colnames<-
Execution halted
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RobLoxBioC.Rcheck/00install.out' for details.
'LinkingTo' for 'mgcv' is unused as it has no 'include' directory
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/ROracle.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   2.2Mb
Error(s) in re-building vignettes:
--- re-building 'data_mashups.Rmd' using rmarkdown
Quitting from lines 91-92 (data_mashups.Rmd) 
Error: processing vignette 'data_mashups.Rmd' failed with diagnostics:
Timeout was reached: [api.opentreeoflife.org] Connection timed out after 10000 milliseconds
--- failed re-building 'data_mashups.Rmd'

--- re-building 'meta-analysis.Rmd' using rmarkdown
--- finished re-building 'meta-analysis.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs    1.8Mb
    tests   1.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.0Mb
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:

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

    area, select

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

    buffer

> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:raster'

> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  5.07 0.35 5.42 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 'rPref-Ex.R' failed
The error most likely occurred in:

> ### Name: plot_btg
> ### Title: Better-Than-Graphs
> ### Aliases: plot_btg get_btg get_btg_dot
> 
> ### ** Examples
> 
> 
> # pick a small data set and create preference and BTG 
> df <- mtcars[1:10,]
> pref <- high(mpg) * low(wt)
> 
> # directly plot the BTG with row numbers as labels
> # uses Rgraphviz if available and igraph otherwise
> plot_btg(df, pref) 
Warning: multiple methods tables found for 'plot'
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot_btg ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

--- re-building 'visualization.Rmd' using rmarkdown
Quitting from lines 84-85 (visualization.Rmd) 
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'visualization.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Running examples in 'RSDA-Ex.R' failed
The error most likely occurred in:

> ### Name: VeterinaryData
> ### Title: Symbolic interval data example
> ### Aliases: VeterinaryData
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(VeterinaryData)
> VeterinaryData
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'warningc' not found
Calls: <Anonymous> ... do.call -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 40-42 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
object 'warningc' not found
--- 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:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/RSeed.Rcheck/00install.out' for details.
Found the following significant warnings:
   #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.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rsolr.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.4Mb
    libs  17.8Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rstap.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.2Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
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 Under development (unstable) (2019-07-05 r76784)
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_3.7.0
> 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()
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   4.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      8.4Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
Package suggested but not available for checking: 'SnakeCharmR'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Running 'testthat.R' [45s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(RxODE)
  > test_check("RxODE")
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   1.9Mb
Running 'testHeapAddressSanitize.R' [1s]
  Running 'testStackAddressSanitize.R' [1s]
Running the tests in 'tests/testHeapAddressSanitize.R' failed.
Complete output:
  > 
  > library(sanitizers)
  > heapAddressSanitize(42)
Running examples in 'SanzCircos-Ex.R' failed
The error most likely occurred in:

> ### Name: make_circos_links
> ### Title: make_circos_links
> ### Aliases: make_circos_links
> 
> ### ** Examples
> 
> 
> links_df <- data.frame(chrom = c(rep("chr1", 5), rep("chr2", 5)),
+ band = c(rep("band1", 3), rep("band2", 2), "band1", rep("band2", 4)),
+ link = c(1, 2, 3, 1, 2, 1, 1, 3, 4, 5),
+ start = c(1, 3, 5, 10, 35, 1, 5, 8, 13, 15),
+ end = c(3, 5, 10, 35, 39, 5, 8, 13, 15, 21))
> 
> links <- make_circos_links(links_df, "chrom", "band", "link", "start", "end", status = TRUE)
Warning: `as.tibble()` is deprecated as of tibble 2.0.0.
Please use `as_tibble()` instead.
The signature and semantics have changed, see `?as_tibble`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error: Assigned data `as.character(df[[chromosome_grouping]][i])` must be compatible with existing data.
i Error occurred for column `V2`.
x Lossy cast from `value` <character> to `x` <logical>.
* Locations: 1.
Backtrace:
     x
  1. \-SanzCircos::make_circos_links(...)
  2.   +-dplyr::bind_rows(...)
  3.   | +-dplyr:::flatten_bindable(dots_values(...))
  4.   | \-rlang::dots_values(...)
  5.   \-pbapply::pblapply(...)
  6.     \-base::lapply(X, FUN, ...)
  7.       \-SanzCircos:::FUN(X[[i]], ...)
  8.         +-base::`[<-`(`*tmp*`, 1, 2, value = "chr1")
  9.         \-tibble:::`[<-.tbl_df`(`*tmp*`, 1, 2, value = "chr1")
 10.           \-tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 11.             \-tibble:::tbl_subassign_row(xj, i, value, value_arg)
 12.               \-base::tryCatch(...)
 13.                 \-base:::tryCatchList(expr, classes, parentenv, handlers)
 14.                   \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.  
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.1Mb
prime.factor: no visible global function definition for 'data'
prime.factor: no visible binding for global variable 'primlist'
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/scmamp.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'Data_loading_and_manipulation.Rmd' using rmarkdown
--- finished re-building 'Data_loading_and_manipulation.Rmd'

--- re-building 'Statistical_assessment_of_the_differences.Rmd' using rmarkdown
Quitting from lines 160-163 (Statistical_assessment_of_the_differences.Rmd) 
Error: processing vignette 'Statistical_assessment_of_the_differences.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'Statistical_assessment_of_the_differences.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/scMappR.Rcheck/00install.out' for details.
Running examples in 'scriptexec-Ex.R' failed
The error most likely occurred in:

> ### Name: execute
> ### Title: Executes a script and returns the output. The stdout and stderr
> ###   are captured and returned. In case of errors, the exit code will
> ###   return in the status field.
> ### Aliases: execute
> 
> ### ** Examples
> 
> library('scriptexec')
> library('testthat')
> 
> # execute script text
> output <- scriptexec::execute('echo command1\necho command2')
> expect_equal(output$status, 0)
> expect_equal(grepl('command1', output$output), TRUE)
Error: grepl("command1", output$output) not equal to TRUE.
1 element mismatch
Execution halted
Error(s) in re-building vignettes:
--- re-building 'scriptexec.Rmd' using rmarkdown
Quitting from lines 24-62 (scriptexec.Rmd) 
Error: processing vignette 'scriptexec.Rmd' failed with diagnostics:
grepl("command1", output$output) not equal to TRUE.
1 element mismatch
--- failed re-building 'scriptexec.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Running examples in 'secret-Ex.R' failed
The error most likely occurred in:

> ### Name: add_travis_user
> ### Title: Add a user via their Travis repo.
> ### Aliases: add_travis_user
> 
> ### ** Examples
> 
> vault <- file.path(tempdir(), ".vault")
> create_vault(vault)
> 
> add_travis_user("gaborcsardi/secret", vault = vault)
Error in open.connection(con, "rb") : HTTP error 404.
Calls: add_travis_user ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.0Mb
Package which this enhances but not available for checking: 'doMC'
Running examples in 'seeclickfixr-Ex.R' failed
The error most likely occurred in:

> ### Name: list_places
> ### Title: Query sub-city neighborhoods in which issues can be reported.
> ### Aliases: list_places
> 
> ### ** Examples
> 
> list_places("Boston, MA",limit = 5)
Error in function (type, msg, asError = TRUE)  : 
  Unknown SSL protocol error in connection to seeclickfix.com:443 
Calls: list_places -> <Anonymous> -> curlPerform -> <Anonymous> -> fun
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SeqFeatR.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'different_thinners.Rmd' using rmarkdown
--- finished re-building 'different_thinners.Rmd'

--- re-building 'simulate_rnaseq.Rmd' using rmarkdown
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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

Loading required package: S4Vectors
Error: package or namespace load failed for 'S4Vectors':
 .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Quitting from lines 82-84 (simulate_rnaseq.Rmd) 
Error: processing vignette 'simulate_rnaseq.Rmd' failed with diagnostics:
package 'S4Vectors' could not be loaded
--- failed re-building 'simulate_rnaseq.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SeqGrapheR.Rcheck/00install.out' for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/seqmagick.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
    libs   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/sequenza.Rcheck/00install.out' for details.
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible global function definition for 'dev.list'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
Package suggested but not available for checking: 'loomR'
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/Seurat.Rcheck/00install.out' for details.
Package unavailable to check Rd xrefs: 'loomR'
installed size is 95.3Mb
  sub-directories of 1Mb or more:
    doc     11.9Mb
    gdal     3.9Mb
    libs    70.1Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   7.3Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    www   8.0Mb
Error(s) in re-building vignettes:
--- re-building 'animate.Rmd' using rmarkdown
--- finished re-building 'animate.Rmd'

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

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

--- re-building 'dynamic.Rmd' using rmarkdown
Quitting from lines 27-45 (dynamic.Rmd) 
Error: processing vignette 'dynamic.Rmd' failed with diagnostics:
Assigned data `runif(15, 500, 750)` must be compatible with existing data.
x Existing data has 75 rows.
x Assigned data has 15 rows.
i Only vectors of size 1 are recycled.
--- failed re-building 'dynamic.Rmd'

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

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

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Signac.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SIGN.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SigTree.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'MCSE.Rmd' using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'kableExtra'

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

    group_rows

--- finished re-building 'MCSE.Rmd'

Warning in file(con, "r") :
  cannot open file 'D:\temp\RtmpC4agmf\file2211c690a611b': Permission denied
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> readLines -> file
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
--- re-building 'simPATHy.Rmd' using rmarkdown
Quitting from lines 252-258 (simPATHy.Rmd) 
Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
package or namespace load failed for 'topologyGSA':
 .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
--- failed re-building 'simPATHy.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package vignette with placeholder title 'Vignette Title':
  'SimplifyStats_Vignette.Rmd'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SimRAD.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/SimReg.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'SimReg-Introduction.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 74-75 (SimReg-Introduction.Rmd) 
Error: processing vignette 'SimReg-Introduction.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'SimReg-Introduction.Rmd'

--- re-building 'SimReg-Priors.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'SimReg-Priors.Rmd'

SUMMARY: processing the following file failed:
  'SimReg-Introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(simrel)
  > 
  > test_check("simrel")
  -- 1. Error: Prepare Design (@test-utils.R#44)  --------------------------------
  Can't join on 'q' x 'q' because of incompatible types (list / list)
  Backtrace:
   1. testthat::expect_identical(prepare_design(opts), dgn)
   3. testthat:::compare.default(act$val, exp$val)
   5. dplyr:::all.equal.tbl_df(x, y, ...)
   6. dplyr:::equal_data_frame(...)
  
  == testthat results  ===========================================================
  [ OK: 169 | SKIPPED: 21 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: Prepare Design (@test-utils.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   2.5Mb
Running examples in 'sisal-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.sisal
> ### Title: Plotting Sequential Input Selection Results
> ### Aliases: plot.sisal
> ### Keywords: hplot graphs IO
> 
> ### ** Examples
> 
> library(graphics)
> foo <- testSisal(dataset="toy", Mtimes=10)
Dataset is "toy"
See ?toy.learn for a description of the data
Adding noise with standard deviation 0.200000
Calling sisal

pruning.criterion=round robin, Mtimes=10, kfold=10, hbranches=1, max.width=1, 
q=0.165, standardize=TRUE, pruning.keep.best=TRUE, pruning.reverse=FALSE, 
use.ridge=FALSE, sp=-1
There are 10 variables and 1000 samples.
There are no missing values.
================================================================================
> ## Plotting the search graph requires "Rgraphviz" and "graph"
> if (requireNamespace("Rgraphviz", quietly=TRUE) &&
+     requireNamespace("graph", quietly=TRUE)) {
+     plot(foo, which=2)
+ }
Warning: multiple methods tables found for 'plot'
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot ... do.call -> <Anonymous> -> plot.default -> xy.coords
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:
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ss.study.ca
> ### Title: Graphs and figures for a Capability Study
> ### Aliases: ss.study.ca
> 
> ### ** Examples
> 
> 	ss.study.ca(ss.data.ca$Volume, rnorm(40, 753, 3), 
+ 		LSL = 740, USL = 760, T = 750, alpha = 0.05, 
+  			f.sub = "Winery Project")
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  20.35 0.87 21.46 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 ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SmartSVA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SMITIDstruct.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.6Mb
Warnings in file 'R/replace_special_characters_internal.R':
  unable to translate '<U+00C4>' to native encoding
  unable to translate '<U+00D6>' to native encoding
  unable to translate '<U+00DC>' to native encoding
  unable to translate '<U+00E4>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00FC>' to native encoding
  unable to translate '<U+00DF>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/snplist.Rcheck/00install.out' for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   2.1Mb
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
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using knitr
Sotkanet R tools (C) 2013-2017 rOpenGov
https://github.com/ropengov/sotkanet
Quitting from lines 54-56 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
unexpected character '<'

--- failed re-building 'tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SpatialKDE)
  > 
  > test_check("SpatialKDE")
  -- 1. Error: (unknown) (@test-kde.R#29)  ---------------------------------------
  package 'rgdal' is not available
  Backtrace:
   1. base::suppressWarnings(...)
   3. raster::projectRaster(test_raster, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
   4. raster:::.requireRgdal()
  
  == testthat results  ===========================================================
  [ OK: 14 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-kde.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SpatialKDE)
  > 
  > test_check("SpatialKDE")
  -- 1. Error: (unknown) (@test-kde.R#29)  ---------------------------------------
  package 'rgdal' is not available
  Backtrace:
   1. base::suppressWarnings(...)
   3. raster::projectRaster(test_raster, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
   4. raster:::.requireRgdal()
  
  == testthat results  ===========================================================
  [ OK: 14 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-kde.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.6Mb
Running examples in 'spatial.tools-Ex.R' failed
The error most likely occurred in:

> ### Name: tahoe_highrez_training
> ### Title: Point and polygon files for use with spatial.tools
> ### Aliases: tahoe_highrez_training
> ### Keywords: data
> 
> ### ** Examples
> 
> library("raster")
Loading required package: sp
> library("rgdal")
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: D:/temp/Rtmpi42DNq/RLIBS_1bcb85ed04db/rgdal/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: D:/temp/Rtmpi42DNq/RLIBS_1bcb85ed04db/rgdal/proj
 Linking to sp version: 1.4-1 
> tahoe_highrez_training_polygons <- readOGR(
+ 	dsn=system.file("external", package="spatial.tools"),layer="tahoe_highrez_training")
OGR data source with driver: ESRI Shapefile 
Source: "D:\temp\Rtmpi42DNq\RLIBS_1bcb85ed04db\spatial.tools\external", layer: "tahoe_highrez_training"
with 8 features
It has 2 fields
> spplot(tahoe_highrez_training_polygons,zcol="Class")
Warning in extend.limits(range(as.numeric(z), finite = TRUE)) :
  NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in seq.default(zrng[1], zrng[2], length.out = cuts + 2) : 
  'from' must be a finite number
Calls: spplot ... <Anonymous> -> levelplot.formula -> seq -> seq.default
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   6.3Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    4.9Mb
    help   5.3Mb
    libs   1.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   2.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.6Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   5.2Mb
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #    Copyright 2015 Province of British Columbia
  > #
  > #    Licensed under the Apache License, Version 2.0 (the "License");
  > #    you may not use this file except in compliance with the License.
  > #    You may obtain a copy of the License at
  > #
  > #       http://www.apache.org/licenses/LICENSE-2.0
  > #
  > #    Unless required by applicable law or agreed to in writing, software
  > #    distributed under the License is distributed on an "AS IS" BASIS,
  > #    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  > #    See the License for the specific language governing permissions and
  > #    limitations under the License.
  > 
  > library(testthat)
  > library(ssdtools)
  
  Attaching package: 'ssdtools'
  
  The following objects are masked from 'package:stats':
  
      dgamma, dweibull, pgamma, pweibull, qgamma, qweibull, rgamma,
      rweibull
  
  > 
  > test_check("ssdtools")
  -- 1. Failure: ssd_gof fitdistscens (@test-gof.R#46)  --------------------------
  as.data.frame(ssd_gof(fluazinam_dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  -- 2. Failure: manual (@test-schwarz-tillmans.R#24)  ---------------------------
  as.data.frame(ssd_gof(dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  == testthat results  ===========================================================
  [ OK: 269 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 2 ]
  1. Failure: ssd_gof fitdistscens (@test-gof.R#46) 
  2. Failure: manual (@test-schwarz-tillmans.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde: no visible global function definition for 'quantile'
stkde: no visible global function definition for 'heat.colors'
stkde: no visible global function definition for 'par'
stkde: no visible global function definition for 'image'
stkde: no visible global function definition for 'contour'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
stkde.sig: no visible global function definition for 'quantile'
stkde.sig: no visible global function definition for 'heat.colors'
stkde.sig: no visible global function definition for 'par'
stkde.sig: no visible global function definition for 'image'
stkde.sig: no visible global function definition for 'contour'
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   9.4Mb
Package required and available but unsuitable version: 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   1.9Mb
    nc    4.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
Running examples in 'statsr-Ex.R' failed
The error most likely occurred in:

> ### Name: bandit_posterior
> ### Title: bandit posterior
> ### Aliases: bandit_posterior
> 
> ### ** Examples
> 
> data = data.frame(machine = c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), 
+                   outcome = c("W", "L", "W", "L", "L", "W", "L", "L", "L", "W"))
> bandit_posterior(data)
m1_good m2_good 
    0.5     0.5 
> plot_bandit_posterior(data)
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error: Assigned data `prior` must be compatible with row subscript `1`.
x 1 row must be assigned.
x Assigned data has 2 rows.
i Only vectors of size 1 are recycled.
Backtrace:
    x
 1. \-statsr::plot_bandit_posterior(data)
 2.   +-base::`[<-`(...)
 3.   \-tibble:::`[<-.tbl_df`(...)
 4.     \-tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       \-tibble:::vectbl_recycle_rhs(...)
 6.         \-base::tryCatch(...)
 7.           \-base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               \-value[[3L]](cond)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'stmVignette.Rnw' using Sweave
stm v1.3.5 successfully loaded. See ?stm for help. 
 Papers, resources, and other materials at structuraltopicmodel.com

Error: processing vignette 'stmVignette.Rnw' failed with diagnostics:
 chunk 7 
Error in load(url("http://goo.gl/VPdxlS")) : 
  error reading from connection

--- failed re-building 'stmVignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.6Mb
Package suggested but not available for checking: 'BSgenome.Ptroglodytes.UCSC.panTro5'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/STRAH.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.8Mb
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/STRMPS.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/StroupGLMM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SubVis.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.2Mb
    libs   1.7Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
dlgMessage.tcltkGUI: no visible global function definition for
  'bringToTop'
Undefined global functions or variables:
  alarm bringToTop
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("utils", "alarm")
to your NAMESPACE file.
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running examples in 'SWMPrExtension-Ex.R' failed
The error most likely occurred in:

> ### Name: seasonal_dot
> ### Title: Seasonal Dot Plot
> ### Aliases: seasonal_dot seasonal_dot.swmpr
> 
> ### ** Examples
> 
> dat_wq <- elksmwq
> #dat_wq <- subset(dat_wq, subset = c('2010-01-01 0:00', '2017-01-01 0:00'))
> dat_wq <- qaqc(dat_wq, qaqc_keep = c(0, 3, 5))
> 
> x <-
+   seasonal_dot(dat_wq, param = 'do_mgl'
+                , lm_trend = TRUE
+                , lm_lab = TRUE
+                , plot_title = TRUE)
Error: Aesthetics must be either length 1 or the same as the data (48): y
Backtrace:
    x
 1. +-SWMPrExtension::seasonal_dot(...)
 2. \-SWMPrExtension:::seasonal_dot.swmpr(...)
 3.   +-ggplot2::ggplot_build(plt)
 4.   \-ggplot2:::ggplot_build.ggplot(plt)
 5.     \-ggplot2:::by_layer(function(l, d) l$compute_aesthetics(d, plot))
 6.       \-ggplot2:::f(l = layers[[i]], d = data[[i]])
 7.         \-l$compute_aesthetics(d, plot)
 8.           \-ggplot2:::f(..., self = self)
 9.             \-ggplot2:::check_aesthetics(evaled, n)
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Running 'spelling.R' [1s]
  Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sys)
  > 
  > test_check("sys")
  -- 1. Failure: exec timeout works (@test-timeout.R#21)  ------------------------
  times[["elapsed"]] is not more than 0.5. Difference: -0.02
  
  == testthat results  ===========================================================
  [ OK: 48 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: exec timeout works (@test-timeout.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
Package suggested but not available for checking: 'duckdb'
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(taxa)
  
  Attaching package: 'taxa'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("taxa")
  -- 1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  -- 2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  -- 3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  == testthat results  ===========================================================
  [ OK: 607 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#52) 
  2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#56) 
  3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/TcGSA.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.9Mb
    libs   1.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.8Mb
installed size is 83.1Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    gdal   3.8Mb
    libs  71.8Mb
    proj   5.0Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs      13.3Mb
    tessdata  14.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    2.9Mb
    libs   1.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
Running examples in 'tidygenomics-Ex.R' failed
The error most likely occurred in:

> ### Name: genome_complement
> ### Title: Calculates the complement to the intervals covered by the
> ###   intervals in a data frame. It can optionally take a 'chromosome_size'
> ###   data frame that contains 2 or 3 columns, the first the names of
> ###   chromosome and in case there are 2 columns the size or first the
> ###   start index and lastly the end index on the chromosome.
> ### Aliases: genome_complement
> 
> ### ** Examples
> 
> 
> library(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

> 
> x1 <- data.frame(id = 1:4, bla=letters[1:4],
+                  chromosome = c("chr1", "chr1", "chr2", "chr1"),
+                  start = c(100, 200, 300, 400),
+                  end = c(150, 250, 350, 450))
> 
> genome_complement(x1, by=c("chromosome", "start", "end"))
Error: .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Execution halted
Error(s) in re-building vignettes:
--- re-building 'intro.Rmd' using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 55-66 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
--- failed re-building 'intro.Rmd'

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

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

> ### Name: heatmap
> ### Title: Creates a 'ComplexHeatmap' plot from 'tbl'
> ### Aliases: heatmap
> 
> ### ** Examples
> 
> 
> library(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

> tidyHeatmap::N52 %>%
+ group_by( `Cell type`) %>%
+ tidyHeatmap::heatmap(
+  .horizontal = UBR,
+  .vertical = symbol_ct,
+  .abundance = `read count normalised log`,
+  annotation = CAPRA_TOTAL
+ )
Adding missing grouping variables: `Cell type`
Error: `width` should be an absolute unit.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using knitr
Quitting from lines 55-63 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
width of the annotation can only be an absolute unit.
--- failed re-building 'introduction.Rmd'

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

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

> ### Name: plot_difference
> ### Title: Plot difference smooth from a GAM.
> ### Aliases: plot_difference
> 
> ### ** Examples
> 
> library(mgcv)
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
> set.seed(10)
> data <- gamSim(4)
Factor `by' variable example
> model <- gam(y ~ fac + s(x2) + s(x2, by = fac) + s(x0), data = data)
> 
> plot_difference(model, x2, list(fac = c("1", "2")))
Error in table(predictors$Terms) - table(predictors[predictors$Label %in%  : 
  non-conformable arrays
Calls: plot_difference -> %>% -> eval -> eval
Execution halted
Error(s) in re-building vignettes:
--- re-building 'plot-smooths.Rmd' using rmarkdown
Quitting from lines 172-177 (plot-smooths.Rmd) 
Error: processing vignette 'plot-smooths.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building 'plot-smooths.Rmd'

--- re-building 'predict-gam.Rmd' using rmarkdown
--- finished re-building 'predict-gam.Rmd'

SUMMARY: processing the following file failed:
  'plot-smooths.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [21s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  -- 1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15)  ----
  paste(as.character(ovid[[1]]), collapse = " ") not equal to td$text[1].
  names for current but not for target
  
  == testthat results  ===========================================================
  [ OK: 297 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Tnseq.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/tolBasis.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/topologyGSA.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/trackr.Rcheck/00install.out' for details.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/treeDA.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   1.5Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  11.5Mb
Running examples in 'tricolore-Ex.R' failed
The error most likely occurred in:

> ### Name: ColorKeySextant
> ### Title: Sextant Scheme Legend
> ### Aliases: ColorKeySextant
> ### Keywords: internal
> 
> ### ** Examples
> 
> tricolore:::ColorKeySextant(center = prop.table(runif(3)),
+                            values = c('#01A0C6', '#B8B3D8', '#F11D8C',
+                                       '#FFB3B3', '#FFFF00', '#B3DCC3'),
+                            label_as = 'pct_diff', show_center = TRUE)
Error in (function (el, elname)  : 
  "plot.title.position" is not a valid theme element name.
Calls: <Anonymous> ... update_theme -> do.call -> <Anonymous> -> mapply -> <Anonymous>
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tricolore)
  > 
  > test_check('tricolore')
  -- 1. Error: NA, Inf, NaNs in input return NA in output (@test-global.R#82)  ---
  "plot.title.position" is not a valid theme element name.
  Backtrace:
   1. tricolore::Tricolore(P, "a", "b", "c", breaks = Inf)
   2. tricolore:::ColorKeyTricolore(...)
   3. tricolore:::BasicKey(...)
   4. ggtern:::`+.gg`(...)
   5. ggtern:::add_ggplot(e1, e2, e2name)
   6. ggtern:::update_theme(p$theme, object)
   9. base::mapply(validate_element, elements, names(elements))
  
  == testthat results  ===========================================================
  [ OK: 33 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: NA, Inf, NaNs in input return NA in output (@test-global.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'choropleth_maps_with_tricolore.Rmd' using rmarkdown
Quitting from lines 28-32 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
All columns in a tibble must be vectors.
x Column `geometry` is a `sfc_MULTIPOLYGON/sfc` object.
--- failed re-building 'choropleth_maps_with_tricolore.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/tth.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ttScreening.Rcheck/00install.out' for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc     6.4Mb
    ubinc   2.0Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs        4.2Mb
installed size is 82.4Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.3Mb
    gdal      3.8Mb
    libs     69.0Mb
    proj      5.0Mb
Running examples in 'unifDAG-Ex.R' failed
The error most likely occurred in:

> ### Name: unifDAG
> ### Title: Uniform Sampling of Directed Acyclic Graphs (DAG)
> ### Aliases: unifDAG unifDAG.approx
> ### Keywords: graphs models
> 
> ### ** Examples
> 
> set.seed(123)
> dag1 <- unifDAG(n=10)
> dag2 <- unifDAG.approx(n=10, n.exact=5)
> 
> dag <- unifDAG(n=5)
> if (require("Rgraphviz")) plot(dag)
Loading required package: Rgraphviz
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

Loading required package: grid
Warning: multiple methods tables found for 'plot'
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot -> plot -> plot.default -> xy.coords
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs   2.3Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
Running examples in 'ushr-Ex.R' failed
The error most likely occurred in:

> ### Name: summarize_model
> ### Title: Summarize model output
> ### Aliases: summarize_model
> 
> ### ** Examples
> 
> 
> set.seed(1234567)
> 
> simulated_data <- simulate_data(nsubjects = 20)
Joining, by = "id"
> 
> model_output <- ushr(data = simulated_data)
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
> 
> summarize_model(model_output, data = simulated_data)
Joining, by = c("id", "Model")
Joining, by = "id"
Error: Assigned data `values` must be compatible with existing data.
i Error occurred for column `ShortLifespan`.
x No common type for `value` <character> and `x` <double>.
Backtrace:
     x
  1. \-ushr::summarize_model(model_output, data = simulated_data)
  2.   \-`%>%`(...)
  3.     +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4.     \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.         \-ushr:::`_fseq`(`_lhs`)
  7.           \-magrittr::freduce(value, `_function_list`)
  8.             +-base::withVisible(function_list[[k]](value))
  9.             \-function_list[[k]](value)
 10.               \-base::replace(., is.na(.), "")
 11.                 +-base::`[<-`(`*tmp*`, list, value = "")
 12.                 \-tibble:::`[<-.tbl_df`(`*tmp*`, list, value = "")
 13.                   \-tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(value))
 14.                     \-base::tryCatch(...)
 15. 
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   6.4Mb
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  23.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/VALERIE.Rcheck/00install.out' for details.
installed size is 79.1Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      3.8Mb
    libs     68.8Mb
    proj      5.0Mb
Running examples in 'vegalite-Ex.R' failed
The error most likely occurred in:

> ### Name: from_spec
> ### Title: Take a JSON Vega-Lite Spec and render as an htmlwidget
> ### Aliases: from_spec
> 
> ### ** Examples
> 
> from_spec("http://rud.is/dl/embedded.json")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung wurde zurückgesetzt.'
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/vhcub.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/viromeBrowser.Rcheck/00install.out' for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.3Mb
    htmlwidgets   3.9Mb
Error(s) in re-building vignettes:
--- re-building 'vortexRguide.Rmd' using rmarkdown
Quitting from lines 293-297 (vortexRguide.Rmd) 
Error: processing vignette 'vortexRguide.Rmd' failed with diagnostics:
Some items of .SDcols are not column names: [N]
--- failed re-building 'vortexRguide.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/VSE.Rcheck/00install.out' for details.
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   6.3Mb
Error(s) in re-building vignettes:
--- re-building 'wCorrArguments.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrArguments_files/figure-latex/ML\%20RMSE\%20plot-1.
pdf' not found.

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

--- re-building 'wCorrFormulas.Rmd' using rmarkdown
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrFormulas_files/figure-latex/bias\%20Versus\%20rho-
1.pdf' not found.

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

SUMMARY: processing the following files failed:
  'wCorrArguments.Rmd' 'wCorrFormulas.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/WGCNA.Rcheck/00install.out' for details.
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wilson)
  
  Attaching package: 'wilson'
  
  The following object is masked from 'package:stats':
  
      heatmap
  
  > 
  > test_check("wilson")
  -- 1. Error: complexHeatmap is downloadable (@test-download.R#31)  -------------
  width of the annotation can only be an absolute unit.
  Backtrace:
   1. ComplexHeatmap::Heatmap(mtcars)
   2. ComplexHeatmap::anno_text(...)
   3. ComplexHeatmap::AnnotationFunction(...)
   4. ComplexHeatmap:::anno_width_and_height(...)
   5. ComplexHeatmap:::stop_wrap("width of the annotation can only be an absolute unit.")
  
  Error : width of the annotation can only be an absolute unit.
  [1] "Error : width of the annotation can only be an absolute unit.\n"
  attr(,"class")
  [1] "try-error"
  attr(,"condition")
  <simpleError: width of the annotation can only be an absolute unit.>
  == testthat results  ===========================================================
  [ OK: 54 | SKIPPED: 5 | WARNINGS: 22 | FAILED: 1 ]
  1. Error: complexHeatmap is downloadable (@test-download.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    bn   7.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0/x13binary.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    java  26.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          4.2Mb
Found the following significant warnings:
  Warning: replacing previous import 'lubridate::intersect' by 'raster::intersect' when loading 'xROI'
  Warning: replacing previous import 'lubridate::union' by 'raster::union' when loading 'xROI'
See 'd:/Rcompile/CRANpkg/local/4.0/xROI.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/AbsFilterGSEA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/adaptiveGPCA.Rcheck/00install.out' for details.
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("aemo")
  Loading required package: aemo
  -- 1. Failure: AEMO data URLs still correct (@test-aemo.R#34)  -----------------
  GET(co_url)$status not equal to 200.
  1/1 mismatches
  [1] 404 - 200 == 204
  
  == testthat results  ===========================================================
  [ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: AEMO data URLs still correct (@test-aemo.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB

Error in scalaConnect(details) : Error in scalaConfig(FALSE): 

<<<<<<<<<<
<<<<<<<<<<
<<<<<<<<<<

Scala is not found!  Please run 'rscala::scalaConfig(download="scala")'

>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>

Execution halted
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB

Error in scalaConnect(details) : Error in scalaConfig(FALSE): 

<<<<<<<<<<
<<<<<<<<<<
<<<<<<<<<<

Scala is not found!  Please run 'rscala::scalaConfig(download="scala")'

>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>

Calls: <Anonymous> ... get -> +.rscalaBridge -> scalaInvoke -> scalaConnect
Execution halted
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB

Warning in exists(n, envir = w$globalenv, mode = "function") :
  restarting interrupted promise evaluation
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB

Warning in exists(n, envir = w$globalenv, mode = "function") :
  restarting interrupted promise evaluation
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB

Warning in get(n, envir = env) :
  restarting interrupted promise evaluation
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB

Error in scalaConnect(details) : Error in scalaConfig(FALSE): 

<<<<<<<<<<
<<<<<<<<<<
<<<<<<<<<<

Scala is not found!  Please run 'rscala::scalaConfig(download="scala")'

>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>

Calls: <Anonymous> ... get -> +.rscalaBridge -> scalaInvoke -> scalaConnect
Execution halted
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB

Error in scalaConnect(details) : Error in scalaConfig(FALSE): 

<<<<<<<<<<
<<<<<<<<<<
<<<<<<<<<<

Scala is not found!  Please run 'rscala::scalaConfig(download="scala")'

>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>

Calls: <Anonymous> ... get -> +.rscalaBridge -> scalaInvoke -> scalaConnect
Execution halted
Running 'testthat.R' [21s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("aibd")
  Loading required package: aibd
  trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
  Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
  ==================================================
  downloaded 18.8 MB
  
  Error in scalaConnect(details) : Error in scalaConfig(FALSE): 
  
  <<<<<<<<<<
  <<<<<<<<<<
  <<<<<<<<<<
  
  Scala is not found!  Please run 'rscala::scalaConfig(download="scala")'
  
  >>>>>>>>>>
  >>>>>>>>>>
  >>>>>>>>>>
  
  Calls: test_check ... as.list.environment -> +.rscalaBridge -> scalaInvoke -> scalaConnect
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'ALA4R.Rmd' using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: maps
Quitting from lines 198-205 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
invalid 'times' argument
--- failed re-building 'ALA4R.Rmd'

SUMMARY: processing the following file failed:
  'ALA4R.Rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/aliases2entrez.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs     4.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.4Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(aoos)
  > 
  > test_check("aoos")
  -- 1. Failure: Type inheritance (@test-S4-types.R#75)  -------------------------
  inherits(Child(), "Test2") isn't true.
  
  -- 2. Failure: Type with VIRTUAL (@test-S4-types.R#111)  -----------------------
  names(Test(x = 2)) == "x" isn't true.
  
  -- 3. Failure: Type with VIRTUAL (@test-S4-types.R#112)  -----------------------
  inherits(Test(), "Type") isn't true.
  
  == testthat results  ===========================================================
  [ OK: 187 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Type inheritance (@test-S4-types.R#75) 
  2. Failure: Type with VIRTUAL (@test-S4-types.R#111) 
  3. Failure: Type with VIRTUAL (@test-S4-types.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 73.7Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  69.5Mb
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(apex)
  Loading required package: ape
  Loading required package: phangorn
  > 
  > test_check("apex")
  -- 1. Error: (unknown) (@test_export.R#8)  -------------------------------------
  subscript out of bounds
  Backtrace:
   1. apex::multidna2genind(x, mlst = TRUE, gapIsNA = TRUE)
   2. adegenet::df2genind(xdfnum, ploidy = 1, ind.names = x@labels)
   3. base::vapply(...)
   4. adegenet:::FUN(X[[i]], ...)
   5. base::rowSums(out[, i, drop = FALSE], na.rm = TRUE)
   6. base::is.data.frame(x)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 1 ]
  1. Error: (unknown) (@test_export.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/apmsWAPP.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ArrayBin.Rcheck/00install.out' for details.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    libs  24.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      2.1Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    bin   22.9Mb
    misc   2.1Mb
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/4.0gcc8/audio.Rcheck/00install.out' for details.
Running examples in 'autocogs-Ex.R' failed
The error most likely occurred in:

> ### Name: cog_spec
> ### Title: Cognostic Specification
> ### Aliases: cog_spec as_cog_specs
> 
> ### ** Examples
> 
> # example cog specifications
> # display like normal
> cog_spec(); TRUE
$keep_layer
[1] TRUE

$remove
character(0)

attr(,"class")
[1] "cog_spec"
[1] TRUE
> # remove scagnostics
> cog_spec(scagnostics = FALSE)
$keep_layer
[1] TRUE

$remove
[1] "scagnostics"

attr(,"class")
[1] "cog_spec"
> # remove layer
> cog_spec(.keep_layer = FALSE); FALSE
$keep_layer
[1] FALSE

$remove
character(0)

attr(,"class")
[1] "cog_spec"
[1] FALSE
> 
> # set up data
> p <- ggplot2::qplot(Sepal.Length, Sepal.Width, data = iris, geom = c("point", "smooth"))
> dt <- tibble::data_frame(panel = list(p))
Warning: `data_frame()` is deprecated, use `tibble()`.
This warning is displayed once per session.
> 
> # compute cognostics like normal
> add_panel_cogs(dt)
Error in switch(as.character(layer$stat_params$method), loess = "geom_smooth_loess",  : 
  EXPR must be a length 1 vector
Calls: add_panel_cogs ... get_layer_info -> layer_info -> layer_info.ggplot -> lapply -> FUN
Execution halted
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(autocogs)
  > 
  > test_check("autocogs")
  -- 1. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246)  ---------------------
  EXPR must be a length 1 vector
  Backtrace:
    1. ggplot2::qplot(cty, hwy, data = mpg, geom = "smooth")
    9. autocogs:::expect_auto_cogs(...)
   11. autocogs:::plot_cogs(.)
   19. autocogs:::get_layer_info(p, keep = keep_layers, ...)
   21. autocogs:::layer_info.ggplot(p, keep = keep, ...)
   22. base::lapply(...)
   23. autocogs:::FUN(X[[i]], ...)
  
  == testthat results  ===========================================================
  [ OK: 242 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/AutoPipe.Rcheck/00install.out' for details.
Running examples in 'autothresholdr-Ex.R' failed
The error most likely occurred in:

> ### Name: auto_thresh
> ### Title: Automatically threshold an array of non-negative integers.
> ### Aliases: auto_thresh auto_thresh_mask auto_thresh_apply_mask mask
> ###   apply_mask
> 
> ### ** Examples
> 
> img_location <- system.file("extdata", "eg.tif", package = "autothresholdr")
> img <- ijtiff::read_tif(img_location)
Running 'spelling.R' [0s]
  Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(autothresholdr)
  > 
  > test_check("autothresholdr")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BACA.Rcheck/00install.out' for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BALCONY.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BALD.Rcheck/00install.out' for details.
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bapred.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   2.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BASiNET.Rcheck/00install.out' for details.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.5Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BayesNetBP.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   4.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BcDiag.Rcheck/00install.out' for details.
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.9.0 is loaded.
  For more information on NIMBLE and a User Manual,
  please visit http://R-nimble.org.
  
  Attaching package: 'nimble'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("bcgam")
  thin = 1: tau, betalpha, sigma, eta
  -- 1. Error: (unknown) (@testthat.R#3)  ----------------------------------------
  unable to load shared object 'D:/temp/RtmpsTDWYx/nimble_generatedCode/dynamicRegistrations_03_28_23_11_48.dll':
    LoadLibrary failure:  Das angegebene Modul wurde nicht gefunden.
  Backtrace:
   1. bcgam::bcgam(...)
   2. bcgam:::bcgam.fit(...)
   3. nimble::compileNimble(gaus)
   4. project$compileModel(units[[i]], control = control, showCompilerOutput = showCompilerOutput)
   5. cppProj$compileFile(compileList, showCompilerOutput)
   6. nimble:::compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
   7. nimble:::compileStaticCode(dllName, cppName, showCompilerOutput)
   8. base::dyn.load(ssDllName, local = TRUE)
   9. base:::inDL(x, as.logical(local), as.logical(now), ...)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@testthat.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: replacing previous import 'sf::st_make_valid' by 'lwgeom::st_make_valid' when loading 'bdl'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bdl.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/beadarrayFilter.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/beadarrayMSV.Rcheck/00install.out' for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 132.1Mb
  sub-directories of 1Mb or more:
    include  131.2Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BiDAG.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.1Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/biganalytics.Rcheck/00install.out' for details.
Running examples in 'bigchess-Ex.R' failed
The error most likely occurred in:

> ### Name: browse_opening
> ### Title: Browse opening
> ### Aliases: browse_opening
> 
> ### ** Examples
> 
> f <- system.file("extdata", "Kasparov.gz", package = "bigchess")
> con <- gzfile(f,encoding = "latin1")
> df <- read.pgn(con,quiet = TRUE,ignore.other.games = TRUE,stat.moves = FALSE)
> # Analyze best Kasparov openings:
> bo <- browse_opening(subset(df,grepl("Kasparov",White)))
Error in UseMethod("droplevels") : 
  no applicable method for 'droplevels' applied to an object of class "character"
Calls: browse_opening -> tree_move -> droplevels
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      2.2Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bigmemory.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.5Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bigtabulate.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BinQuasi.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   2.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Running examples in 'biogram-Ex.R' failed
The error most likely occurred in:

> ### Name: calc_si
> ### Title: Compute similarity index
> ### Aliases: calc_si
> 
> ### ** Examples
> 
> # example from Stephenson & Freeland, 2013 (Fig. 6)
> enc1 <- list(`1` = "A",
+              `2` = c("F", "E"),
+              `3` = c("C", "D", "G"))
> 
> enc2 <- list(`1` = c("A", "G"),
+              `2` = c("C", "D", "E", "F"))
> 
> enc3 <- list(`1` = c("D", "G"),
+              `2` = c("E", "F"),
+              `3` = c("A", "C"))
>              
> calc_si(enc1, enc2)
Error in order(levels(res[["element"]])) : argument 1 is not a vector
Calls: calc_si ... encoding2matrix -> encoding2df -> [ -> [.data.frame -> order
Execution halted
Running examples in 'bioimagetools-Ex.R' failed
The error most likely occurred in:

> ### Name: readTIF
> ### Title: Read tif stacks
> ### Aliases: readTIF
> 
> ### ** Examples
> 
> kringel <- readTIF(system.file("extdata","kringel.tif",package="bioimagetools"))
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/biomartr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BioMedR.Rcheck/00install.out' for details.
Running examples in 'bios2mds-Ex.R' failed
The error most likely occurred in:

> ### Name: bios2mds-package
> ### Title: From BIOlogical Sequences to MultiDimensional Scaling
> ### Aliases: bios2mds-package bios2mds
> ### Keywords: package
> 
> ### ** Examples
> 
> # The MSA files provided with the package correspond to the sequence 
> # alignment of non-olfactory class A G-protein-coupled receptors from
> # H. sapiens and D. melanogaster prepared by Deville et al. (2009).  
> 
> # loading GPCR data
> data(gpcr)
> 
> # building distance matrices between the aligned GPCR sequences from
> # H. sapiens and D. melanogaster
> human <- import.fasta(system.file("msa/human_gpcr.fa", package = "bios2mds"))
> drome <- import.fasta(system.file("msa/drome_gpcr.fa", package = "bios2mds"))
> 
> #active <- mat.dif(human, human)
> # or
> active <- gpcr$dif$sapiens.sapiens
> 
> #sup <- mat.dif(drome, human)
> # or
> sup <- gpcr$dif$melanogaster.sapiens
> 
> # performing MDS analysis of the GPCR sequences from H. sapiens 
> mmds_active <- mmds(active, group.file=system.file(
+ "csv/human_gpcr_group.csv",package = "bios2mds"))
Error in rbind(col, matrix(c(names[i], levels(element[, 2])[element[j,  : 
  number of columns of matrices must match (see arg 2)
Calls: mmds -> col.group -> rbind
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BiSEp.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
plotblockrand: no visible global function definition for 'pdf'
plotblockrand: no visible global function definition for 'dev.off'
plotblockrand: no visible global function definition for 'par'
plotblockrand: no visible global function definition for 'plot.new'
plotblockrand: no visible global function definition for 'strheight'
plotblockrand: no visible global function definition for 'strwidth'
plotblockrand: no visible global function definition for 'text'
plotblockrand: no visible global function definition for 'lines'
Undefined global functions or variables:
  dev.off lines par pdf plot.new strheight strwidth text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot.new", "strheight",
             "strwidth", "text")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BMTME)
  > 
  > test_check("BMTME")
  -- 1. Failure: RandomPartition (@test.R#52)  -----------------------------------
  RP_Test$Environments inherits from `character` not `factor`.
  
  -- 2. Failure: RandomPartition (@test.R#72)  -----------------------------------
  RP_Test2$Traits inherits from `character` not `factor`.
  
  == testthat results  ===========================================================
  [ OK: 164 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: RandomPartition (@test.R#52) 
  2. Failure: RandomPartition (@test.R#72) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BonEV.Rcheck/00install.out' for details.
installed size is 62.4Mb
  sub-directories of 1Mb or more:
    include   8.6Mb
    lib      53.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Brundle.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.7Mb
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/4.0gcc8/Cairo.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cate.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   1.1Mb
    libs      2.2Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.4Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ceg.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   2.9Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CePa.Rcheck/00install.out' for details.
Running examples in 'cgmanalysis-Ex.R' failed
The error most likely occurred in:

> ### Name: cgmreport
> ### Title: Generate AGP
> ### Aliases: cgmreport
> 
> ### ** Examples
> 
> cgmreport(system.file("extdata","Cleaned",package = "cgmanalysis"))
Error in stats::smooth(quartiles$sensorglucose5perc, kind = "3R", twiceit = TRUE) : 
  attempt to smooth NA values
Calls: cgmreport -> <Anonymous>
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.8Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
  Warning: found methods to import for function 'plot' but not the generic itself
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/classGraph.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CleanBSequences.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/clustermole.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CNVScope.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cogmapr.Rcheck/00install.out' for details.
Found the following significant warnings:
  data.table_assign.c:314:93: warning: too many arguments for format [-Wformat-extra-args]
  data.table_assign.c:321:93: warning: too many arguments for format [-Wformat-extra-args]
  data.table_assign.c:327:95: warning: too many arguments for format [-Wformat-extra-args]
  data.table_forder.c:505:10: warning: too many arguments for format [-Wformat-extra-args]
  data.table_forder.c:609:16: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/collapse.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CONDOP.Rcheck/00install.out' for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  == testthat results  ===========================================================
  [ OK: 594 | SKIPPED: 8 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  == testthat results  ===========================================================
  [ OK: 594 | SKIPPED: 8 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    libs      2.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.8Mb
Running examples in 'countToFPKM-Ex.R' failed
The error most likely occurred in:

> ### Name: fpkmheatmap
> ### Title: Convert Counts to Fragments per Kilobase of Transcript per
> ###   Million (FPKM) A FPKM heatmap plot of the highly variable features in
> ###   RNA-Seq dataset
> ### Aliases: fpkmheatmap
> 
> ### ** Examples
> 
> library(countToFPKM)
> 
> file.readcounts <- system.file("extdata", "RNA-seq.read.counts.csv", package="countToFPKM")
> file.annotations <- system.file("extdata", "Biomart.annotations.hg38.txt", package="countToFPKM")
> file.sample.metrics <- system.file("extdata", "RNA-seq.samples.metrics.txt", package="countToFPKM")
> 
> 
> # Import the read count matrix data into R.
> counts <- as.matrix(read.csv(file.readcounts))
> 
> # Import feature annotations. 
> # Assign feature length into a numeric vector.
> gene.annotations <- read.table(file.annotations, sep="\t", header=TRUE)
> featureLength <- gene.annotations$length
> 
> # Import sample metrics. 
> # Assign mean fragment length into a numeric vector.
> samples.metrics <- read.table(file.sample.metrics, sep="\t", header=TRUE)
> meanFragmentLength <- samples.metrics$meanFragmentLength
> 
> # Return FPKM into a numeric matrix.
> fpkm_matrix <- fpkm (counts, featureLength, meanFragmentLength)
> 
> # Plot log10(FPKM+1) heatmap of top 30 highly variable features
> fpkmheatmap(fpkm_matrix, topvar=30, showfeaturenames=TRUE, return_log = TRUE)
Error in as.unit(e2) : old version of unit class is no longer allowed
Calls: fpkmheatmap -> Heatmap -> Ops.unit -> as.unit
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(covid19us)
  > 
  > test_check("covid19us")
  -- 1. Failure: get_states_daily works (@test-all.R#21)  ------------------------
  nrow(too_early) not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  -- 2. Error: other funs work (@test-all.R#53)  ---------------------------------
  Can't subset columns that don't exist.
  x The column `ssl_no_verify` doesn't exist.
  Backtrace:
    1. covid19us::get_tracker_urls()
   30. vctrs:::stop_subscript_oob(...)
   31. vctrs:::stop_subscript(...)
  
  == testthat results  ===========================================================
  [ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: get_states_daily works (@test-all.R#21) 
  2. Error: other funs work (@test-all.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cp4p.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cplexAPI.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CSESA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CSFA.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   4.2Mb
Found the following significant warnings:
  ./src/common/Random.c:105:5: warning: 'memcpy' pointer overflow between offset 0 and size [4294967292, 2147483647] [-Warray-bounds]
  ./src/common/Random.c:105:5: warning: 'memcpy' pointer overflow between offset 0 and size [-4, 9223372036854775807] [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cubature.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   5.5Mb
Found the following significant warnings:
  Warning: No CA bundle found. SSL validation disabled.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/curl.Rcheck/00install.out' for details.
Running 'spelling.R' [0s]
  Running 'testthat.R' [62s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(curl)
  Warning message:
  No CA bundle found. SSL validation disabled. 
  > 
  > # Comply with CRAN policy: skip tests if no internet
  > if(curl::has_internet()){
  +   test_check("curl")
  + }
  This is libcurl version 7.64.1 with OpenSSL/1.1.1a (Schannel) 
  Using test server: http://hb.opencpu.org 
  -- 1. Failure: Invalid domain raises an error (@test-certificates.R#15)  -------
  `curl_fetch_memory(fake_url)` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 218 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Invalid domain raises an error (@test-certificates.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [63s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(curl)
  Warning message:
  No CA bundle found. SSL validation disabled. 
  > 
  > # Comply with CRAN policy: skip tests if no internet
  > if(curl::has_internet()){
  +   test_check("curl")
  + }
  This is libcurl version 7.64.1 with OpenSSL/1.1.1a (Schannel) 
  Using test server: http://hb.opencpu.org 
  -- 1. Failure: Invalid domain raises an error (@test-certificates.R#15)  -------
  `curl_fetch_memory(fake_url)` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 218 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Invalid domain raises an error (@test-certificates.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   2.4Mb
Package required but not available: 'flowDensity'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Found the following significant warnings:
  Warning: No CA bundle found. SSL validation disabled.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CytobankAPI.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: No CA bundle found. SSL validation disabled.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CytobankBridgeR.Rcheck/00install.out' for details.
Running examples in 'DALEXtra-Ex.R' failed
The error most likely occurred in:

> ### Name: explain_scikitlearn
> ### Title: Wrapper for Python Scikit-Learn Models
> ### Aliases: explain_scikitlearn
> 
> ### ** Examples
> 
> library("DALEXtra")
> if(DALEXtra:::is_conda()) {
+    # Explainer build (Keep in mind that 18th column is target)
+    titanic_test <- read.csv(system.file("extdata", "titanic_test.csv", package = "DALEXtra"))
+    # Keep in mind that when pickle is being built and loaded,
+    # not only Python version but libraries versions has to match aswell
+    explainer <- explain_scikitlearn(system.file("extdata", "scikitlearn.pkl", package = "DALEXtra"),
+    yml = system.file("extdata", "testing_environment.yml", package = "DALEXtra"),
+    data = titanic_test[,1:17], y = titanic_test$survived)
+    plot(model_performance(explainer))
+ 
+    # Predictions with newdata
+    predict(explainer, titanic_test[1:10,1:17])
+ 
+ } else {
+   print('Conda is required.')
+ }
There already exists environment named the same as it is specified in .yml file - myenv. It will be used
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe" "D:/temp/RtmpUBjs83/RLIBS_1412cd977702/reticulate/config/config.py"' had status 2
Warning: Error in python_config(python_version, required_module, python_version, : Error 2 occurred running C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe 

Error: Yours environment has to match environment where pickle file was created. It also includes encoding, python version, and libraries version. Specifying .yml file or path to virtual environment may help. For more information look warnings() and then ?explain_scikitlearn
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   2.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DCD.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/dcGOR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DeducerSpatial.Rcheck/00install.out' for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   2.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.2Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(detrendr)
  > 
  > test_check("detrendr")
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/dGAselID.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DGCA.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DiffCorr.Rcheck/00install.out' for details.
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:11153 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11153 (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:11047 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11047 (sockconn)
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   2.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   2.0Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   2.5Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/dlsem.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/dnet.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DRomics.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/dSVA.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.6Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   5.4Mb
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dyndimred)
  > library(dynutils)
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  > 
  > test_check("dyndimred")
  -- 1. Error: Perform dimred dm_destiny  ----------------------------------------
  Please install the following packages: 
    "destiny"
  Backtrace:
   1. dyndimred:::method_fun(expr)
   2. dynutils::install_packages("destiny")
  
  -- 2. Error: Perform dimred dm_destiny  ----------------------------------------
  Please install the following packages: 
    "destiny"
  Backtrace:
   1. dyndimred:::method_fun(small_expr)
   2. dynutils::install_packages("destiny")
  
  == testthat results  ===========================================================
  [ OK: 191 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 2 ]
  1. Error: Perform dimred dm_destiny 
  2. Error: Perform dimred dm_destiny 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    bin       6.1Mb
    extdata   2.9Mb
Found the following significant warnings:
  Warning: replacing previous import 'sf::st_make_valid' by 'lwgeom::st_make_valid' when loading 'edbuildmapr'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/edbuildmapr.Rcheck/00install.out' for details.
Running 'test-all.R' [11s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  -- 1. Failure: moves_calc gets the correct results (@test-calculators.R#210)  --
  `moves` not equal to `correct_result`.
  Component "sid": Modes: character, numeric
  Component "sid": Attributes: < target is NULL, current is list >
  Component "sid": target is character, current is factor
  
  == testthat results  ===========================================================
  [ OK: 509 | SKIPPED: 0 | WARNINGS: 29 | FAILED: 1 ]
  1. Failure: moves_calc gets the correct results (@test-calculators.R#210) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc       5.6Mb
    extdata   5.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/EMA.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.9Mb
Found the following significant warnings:
  Warning: replacing previous import 'lwgeom::st_make_valid' by 'sf::st_make_valid' when loading 'EmissV'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/EmissV.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/empiricalFDR.DESeq2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/EncDNA.Rcheck/00install.out' for details.
Running examples in 'EpiCurve-Ex.R' failed
The error most likely occurred in:

> ### Name: EpiCurve
> ### Title: Plot an Epidemic Curve
> ### Aliases: EpiCurve
> ### Keywords: ~documentation
> 
> ### ** Examples
> 
> # library(Epicurve)
> date <- seq(as.timeDate("2017-05-10 21:35:22"), as.timeDate("2017-05-12 06:15:12"), by="12 min")
> val <- rep(1, length(date))
> tri <- rep(c("Alive", "Died","Unknown"), length.out=length(date))
> DF <- data.frame(date, val, tri)
> names(DF) <- c("date","value", "tri")
> 
> 
> EpiCurve(DF,
+          date = "date",
+          freq = "value",
+          period = "hour",
+          split = 4,
+          cutvar = "tri",
+          ylabel="Number of cases",
+          xlabel= "From 2017-05-10 21:35:22 To 2017-05-12 06:15:12",
+          title = "Epidemic Curve")
Error: Column `DateFactor` is unknown
Execution halted
Error(s) in re-building vignettes:
--- re-building 'EpiCurve.Rmd' using rmarkdown
Loading required package: ggplot2
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: ISOweek
Loading required package: scales
Quitting from lines 149-156 (EpiCurve.Rmd) 
Error: processing vignette 'EpiCurve.Rmd' failed with diagnostics:
Column `DateFactor` is unknown
--- failed re-building 'EpiCurve.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eqn2svg)
  > 
  > test_check("eqn2svg")
  -- 1. Error: SVG conversion works (@test-eqn2svg.R#3)  -------------------------
  cannot open the connection
  Backtrace:
   1. eqn2svg::eqn2svg(eqn = l_time_domain[25], preview = FALSE)
   2. base::readLines(url, warn = FALSE)
   3. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: SVG conversion works (@test-eqn2svg.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eudract)
  > 
  > test_check("eudract")
  -- 1. Error: (unknown) (@test_bea.R#37)  ---------------------------------------
  invalid value for 'stringsAsFactors'
  Backtrace:
   1. base::options(stringsAsFactors = old)
  
  == testthat results  ===========================================================
  [ OK: 53 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: (unknown) (@test_bea.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ExomeDepth.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/exp2flux.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'using_genExPrior.Rmd' using rmarkdown
Quitting from lines 58-59 (using_genExPrior.Rmd) 
Error: processing vignette 'using_genExPrior.Rmd' failed with diagnostics:
unable to load shared object 'D:/temp/RtmpO83Rsm/nimble_generatedCode/dynamicRegistrations_03_29_03_24_05.dll':
  LoadLibrary failure:  Das angegebene Modul wurde nicht gefunden.

--- failed re-building 'using_genExPrior.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.1Mb
Running examples in 'factoextra-Ex.R' failed
The error most likely occurred in:

> ### Name: fviz_mfa
> ### Title: Visualize Multiple Factor Analysis
> ### Aliases: fviz_mfa fviz_mfa_ind fviz_mfa_quali_biplot fviz_mfa_var
> ###   fviz_mfa_axes
> 
> ### ** Examples
> 
> # Compute Multiple Factor Analysis
> library("FactoMineR")
> data(wine)
> res.mfa <- MFA(wine, group=c(2,5,3,10,9,2), type=c("n",rep("s",5)),
+                ncp=5, name.group=c("orig","olf","vis","olfag","gust","ens"),
+                num.group.sup=c(1,6), graph=FALSE)
>                
> # Eigenvalues/variances of dimensions
> fviz_screeplot(res.mfa)
> # Group of variables
> fviz_mfa_var(res.mfa, "group")
> # Quantitative variables
> fviz_mfa_var(res.mfa, "quanti.var", palette = "jco", 
+   col.var.sup = "violet", repel = TRUE)
Error in `[.data.frame`(X$call$X, rownames(ind), grp, drop = FALSE) : 
  undefined columns selected
Calls: fviz_mfa_var ... .add_ind_groups -> as.data.frame -> [ -> [.data.frame
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    Rcgi      2.8Mb
    cgi-bin   2.7Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/fcaR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/FcircSEC.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.4Mb
Found the following sources/headers with CR or CRLF line endings:
  inst/include/fDMA.h
Some Unix compilers require LF line endings.
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/4.0gcc8/FGSG.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   2.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Package required but not available: 'flowWorkspace'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   3.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   2.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/funbarRF.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      2.0Mb
Running 'testthat.R' [22s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(fuzzyjoin)
  > 
  > test_check("fuzzyjoin")
  -- 1. Failure: genome_join throws an error if not given three columns (@test_gen
  `genome_inner_join(x1, x2, by = c("start", "end"))` threw an error with unexpected message.
  Expected match: "three columns"
  Actual message: "genome_join requires the IRanges package: https://bioconductor.org/packages/release/bioc/html/IRanges.html"
  Backtrace:
   1. testthat::expect_error(...)
   6. fuzzyjoin::genome_inner_join(x1, x2, by = c("start", "end"))
   7. fuzzyjoin::genome_join(x, y, by, mode = "inner", ...)
  
  == testthat results  ===========================================================
  [ OK: 230 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: genome_join throws an error if not given three columns (@test_genome_join.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/g2f.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    bin   8.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      5.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is 85.3Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    gdal     3.8Mb
    libs    72.9Mb
    proj     5.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.8Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/geneNetBP.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/geno2proteo.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.0Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GExMap.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ggmsa.Rcheck/00install.out' for details.
Running examples in 'ggpol-Ex.R' failed
The error most likely occurred in:

> ### Name: facet_share
> ### Title: A shared axis for two panels
> ### Aliases: facet_share
> 
> ### ** Examples
> 
> df <- data.frame(age = sample(1:20, 1000, replace = TRUE), 
+                  gender = c("M","F"), levels = c("M", "F"))
> 
> # Get the count per age and sex
> df$count <- 1
> df <- aggregate(count ~ gender + age, data = df, length)
> 
> # For the horizontally shared axis, if we want to mirror the axes,
> # we have to multiply the first panel by -1, and use coord_flip().
> df_h <- df 
> df_h$count = ifelse(df_h$gender == "F", df_h$count * -1, df_h$count)
> 
> p <- ggplot(df_h, aes(x = factor(age), y = count, fill = gender)) + 
+   geom_bar(stat = "identity") +
+   facet_share(~gender, dir = "h", scales = "free", reverse_num = TRUE) + 
+   coord_flip() +
+   labs(x = "Age", y = "Count") + 
+   theme(legend.position = "bottom")
> 
> p
Error in axes$y$left[[1]]$children$axis$grobs[[lab_idx]] : 
  attempt to select less than one element in get1index
Calls: <Anonymous> ... ggplot_gtable.ggplot_built -> <Anonymous> -> f -> <Anonymous> -> f
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ggtern.Rcheck/00install.out' for details.
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    doc         1.2Mb
    libs       21.7Mb
    test_data   1.2Mb
Found the following significant warnings:
  kmppini.cpp:241:14: warning: 'void* memcpy(void*, const void*, size_t)' forming offset [5, 8] is out of the bounds [0, 4] of object 'sed' with type 'std::size_t' {aka 'unsigned int'} [-Warray-bounds]
  kmppini.cpp:275:14: warning: 'void* memcpy(void*, const void*, size_t)' forming offset [5, 8] is out of the bounds [0, 4] of object 'sed' with type 'std::size_t' {aka 'unsigned int'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GMKMcharlie.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GMMAT.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GOGANPA.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: No CA bundle found. SSL validation disabled.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GoogleKnowledgeGraphR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gpuR.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gRain.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gRbase.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gRc.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gridDebug.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gridGraphviz.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gRim.Rcheck/00install.out' for details.
Running examples in 'gtools-Ex.R' failed
The error most likely occurred in:

> ### Name: defmacro
> ### Title: Define a macro
> ### Aliases: defmacro strmacro
> ### Keywords: programming
> 
> ### ** Examples
> 
> ####
> # macro for replacing a specified missing value indicator with NA
> # within a dataframe
> ###
> setNA <- defmacro(df, var, values,
+                   expr={
+                          df$var[df$var %in% values] <- NA
+                        })
> 
> # create example data using 999 as a missing value indicator
> d <- data.frame(
+    Grp=c("Trt", "Ctl", "Ctl", "Trt", "Ctl", "Ctl", "Trt", "Ctl", "Trt", "Ctl"),
+    V1=c(1, 2, 3, 4, 5, 6, 999, 8,   9,  10),
+    V2=c(1, 1, 1, 1, 1, 2, 999, 2, 999, 999)
+                )
> d
   Grp  V1  V2
1  Trt   1   1
2  Ctl   2   1
3  Ctl   3   1
4  Trt   4   1
5  Ctl   5   1
6  Ctl   6   2
7  Trt 999 999
8  Ctl   8   2
9  Trt   9 999
10 Ctl  10 999
> 
> # Try it out
> setNA(d, V1, 999)
> setNA(d, V2, 999)
> d
   Grp V1 V2
1  Trt  1  1
2  Ctl  2  1
3  Ctl  3  1
4  Trt  4  1
5  Ctl  5  1
6  Ctl  6  2
7  Trt NA NA
8  Ctl  8  2
9  Trt  9 NA
10 Ctl 10 NA
> 
> 
> ###
> # Expression macro
> ###
> plot.d <- defmacro( df, var, DOTS, col="red", title="", expr=
+   plot( df$var ~ df$Grp, type="b", col=col, main=title, ... )
+ )
> 
> plot.d( d, V1)
Warning in xy.coords(x, y, xlabel, ylabel, log) :
  NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'xlim' values
Calls: plot.d ... do.call -> plot -> plot.default -> localWindow -> plot.window
Execution halted
Package suggested but not available for checking: 'gt'
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GUIProfiler.Rcheck/00install.out' for details.
installed size is 130.6Mb
  sub-directories of 1Mb or more:
    java  128.5Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/hasseDiagram.Rcheck/00install.out' for details.
Found the following significant warnings:
  readstat/readstat_convert.c:18:42: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:89:17: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:197:17: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/haven.Rcheck/00install.out' for details.
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hazer)
  > 
  > test_check("hazer")
  -- 1. Failure: test the haze (@testall.R#22)  ----------------------------------
  floor(h$haze * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 225, 224).
  1/1 mismatches
  [1] 224 - 225 == -1
  
  -- 2. Failure: test the haze (@testall.R#23)  ----------------------------------
  floor(h$A0 * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 710, 712).
  1/1 mismatches
  [1] 712 - 710 == 2
  
  == testthat results  ===========================================================
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: test the haze (@testall.R#22) 
  2. Failure: test the haze (@testall.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/hddplot.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/HDMT.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
Error(s) in re-building vignettes:
--- re-building 'authentication.Rmd' using rmarkdown
--- finished re-building 'authentication.Rmd'

--- re-building 'geocoder.Rmd' using rmarkdown
Quitting from lines 99-110 (geocoder.Rmd) 
Error: processing vignette 'geocoder.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'geocoder.Rmd'

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

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

--- re-building 'transit.Rmd' using rmarkdown
Quitting from lines 93-109 (transit.Rmd) 
Error: processing vignette 'transit.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'transit.Rmd'

--- re-building 'weather.Rmd' using rmarkdown
Quitting from lines 54-70 (weather.Rmd) 
Error: processing vignette 'weather.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'weather.Rmd'

SUMMARY: processing the following files failed:
  'geocoder.Rmd' 'transit.Rmd' 'weather.Rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/HeritSeq.Rcheck/00install.out' for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/HiCfeat.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
    libs   2.1Mb
Package vignette with placeholder title 'Vignette Title':
  'the_basics.Rmd'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/hoardeR.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/hpoPlot.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   1.8Mb
    libs          3.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   3.0Mb
Running examples in 'hyfo-Ex.R' failed
The error most likely occurred in:

> ### Name: writeNcdf
> ### Title: Write to NetCDF file using hyfo list file
> ### Aliases: writeNcdf
> 
> ### ** Examples
> 
> # First open the test NETcDF file.
> filePath <- system.file("extdata", "tnc.nc", package = "hyfo")
> 
> 
> # Then if you don't know the variable name, you can use \code{getNcdfVar} to get variable name
> varname <- getNcdfVar(filePath)
> 
> nc <- loadNcdf(filePath, varname)
Loading data...
Processing...
> 
> # Then write to your work directory
> 
> writeNcdf(nc, 'test.nc')
Error in Ops.difftime(x, 1) : '%%' not defined for "difftime" objects
Calls: writeNcdf ... getTimeUnit -> sapply -> lapply -> FUN -> Ops.difftime
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ICAMS.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ICDS.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.9Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/iheatmapr.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Running examples in 'ijtiff-Ex.R' failed
The error most likely occurred in:

> ### Name: as_EBImage
> ### Title: Convert an ijtiff_img to an EBImage::Image.
> ### Aliases: as_EBImage
> 
> ### ** Examples
> 
> if (require(EBImage)) {
+   img <- read_tif(system.file("img", "Rlogo.tif", package = "ijtiff"))
+   str(img)
+   str(as_EBImage(img))
+   img <- read_tif(system.file("img", "2ch_ij.tif", package = "ijtiff"))
+   str(img)
+   str(as_EBImage(img))
+ }
Loading required package: EBImage

Attaching package: 'EBImage'

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

    display
Running 'spelling.R' [0s]
  Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ijtiff)
  > 
  > test_check("ijtiff")
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     15.9Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/IMaGES.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/immuneSIM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/INCATome.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.7Mb
Running examples in 'infoDecompuTE-Ex.R' failed
The error most likely occurred in:

> ### Name: summaryAovOnePhase
> ### Title: Summarize an Theoretical Analysis of Variance Model of
> ###   Single-Phase Experiments
> ### Aliases: summaryAovOnePhase
> ### Keywords: design
> 
> ### ** Examples
> 
> 
> design1 <- local({ 
+   Ani = as.factor(LETTERS[c(1,2,3,4,
+                             5,6,7,8)])
+   Trt = as.factor(letters[c(1,1,1,1,
+                             2,2,2,2)])
+   data.frame(Ani, Trt)
+ })
> 
> summaryAovOnePhase(design1, blk.str = "Ani", trt.str = "Trt") 
Error in eigen(t(T) %*% t(N) %*% C %*% N %*% T) : 0 x 0 matrix
Calls: summaryAovOnePhase ... lapply -> FUN -> getEffFactor -> invInfMat -> eigen
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/intePareto.Rcheck/00install.out' for details.
Running 'testthat.R' [113s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(interactions)
  > 
  > test_check("interactions")
  Failed with error:  'there is no package called 'brms''
  -- 1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157)  
  `print(p)` produced messages.
  
  -- 2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162)  
  `print(p)` produced messages.
  
  Failed with error:  'there is no package called 'brms''
  Failed with error:  'there is no package called 'rstanarm''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  == testthat results  ===========================================================
  [ OK: 161 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157) 
  2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ionflows.Rcheck/00install.out' for details.
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:11529 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11529 (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:11243 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11243 (sockconn)
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.1Mb
Error(s) in re-building vignettes:
--- re-building 'isocat.Rmd' using rmarkdown
Quitting from lines 206-214 (isocat.Rmd) 
Error: processing vignette 'isocat.Rmd' failed with diagnostics:
indivIDs must be of class 'vector' or 'factor'.
--- failed re-building 'isocat.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           4.9Mb
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(janitor)
  
  Attaching package: 'janitor'
  
  The following objects are masked from 'package:stats':
  
      chisq.test, fisher.test
  
  > 
  > test_check("janitor")
  -- 1. Failure: totals col is correct (@test-add-totals.R#33)  ------------------
  untabyl(adorn_totals(ct, "col")) not equal to data.frame(...).
  Component "a": Modes: character, numeric
  Component "a": Attributes: < target is NULL, current is list >
  Component "a": target is character, current is factor
  
  -- 2. Failure: values are converted to NAs at the data.frame level (@test-clean-
  cleaned_df[[2]] not equal to factor(c(NA, NA, "b"), levels = c("a", "b")).
  Types not compatible: character is not integer
  
  Reading layer `nc' from data source `D:\temp\Rtmp0kFglj\RLIBS_3203c1a285769\sf\shape\nc.shp' using driver `ESRI Shapefile'
  Simple feature collection with 100 features and 14 fields
  geometry type:  MULTIPOLYGON
  dimension:      XY
  bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
  CRS:            4267
  -- 3. Failure: show_missing_levels parameter works (@test-tabyl.R#216)  --------
  z %>% tabyl(a, b, new, show_missing_levels = TRUE) not equal to list(...).
  Component "lvl1": Attributes: < Component "core": Component "a": 'current' is not a factor >
  Component "lvl1": Component "a": 'current' is not a factor
  
  == testthat results  ===========================================================
  [ OK: 554 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: totals col is correct (@test-add-totals.R#33) 
  2. Failure: values are converted to NAs at the data.frame level (@test-clean-NAs.R#31) 
  3. Failure: show_missing_levels parameter works (@test-tabyl.R#216) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/jetset.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/kangar00.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/kmeRs.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/LANDD.Rcheck/00install.out' for details.
Found the following significant warnings:
  model_simul.cpp:838:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  model_simul.cpp:719:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:720:22: warning: '.bin' directive writing 4 bytes into a region of size between 0 and 8 [-Wformat-overflow=]
  model_simul.cpp:721:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:722:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:723:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:724:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  printReadWrite.cpp:54:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:74:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:84:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:138:38: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:139:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:140:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:141:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:152:91: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/landsepi.Rcheck/00install.out' for details.
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  69.6Mb
    proj   5.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/leapp.Rcheck/00install.out' for details.
Running examples in 'lemon-Ex.R' failed
The error most likely occurred in:

> ### Name: annotate_y_axis
> ### Title: Annotations in the axis
> ### Aliases: annotate_y_axis annotate_x_axis
> 
> ### ** Examples
> 
> library(ggplot2)

Attaching package: 'ggplot2'

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

    element_render

> 
> p <- ggplot(mtcars, aes(mpg, hp, colour=disp)) + geom_point()
> 
> l <- p + annotate_y_axis('mark at', y=200, tick=TRUE)
> l
Error in upgradeUnit.default(list(0, NULL, 1L)) : Not a unit object
Calls: <Anonymous> ... <Anonymous> -> pSummary -> <Anonymous> -> upgradeUnit.default
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lemon)
  > 
  > 
  > if (TRUE) {
  +   test_check("lemon")
  + } #else {
  -- 1. Failure: ggplot2 does not break lemon_plot by altering class (@test_lemon_
  `l + 1` threw an error with unexpected message.
  Expected match: "Don't know how to add 1 to a plot"
  Actual message: "Can't add `1` to a ggplot object."
  Backtrace:
   1. testthat::expect_error(...)
   6. ggplot2:::`+.gg`(l, 1)
   7. ggplot2:::add_ggplot(e1, e2, e2name)
   9. ggplot2:::ggplot_add.default(object, p, objectname)
  
  == testthat results  ===========================================================
  [ OK: 137 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: ggplot2 does not break lemon_plot by altering class (@test_lemon_plot.r#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'capped-axes.Rmd' using rmarkdown
--- finished re-building 'capped-axes.Rmd'

--- re-building 'facet-rep-labels.Rmd' using rmarkdown
--- finished re-building 'facet-rep-labels.Rmd'

--- re-building 'geoms.Rmd' using rmarkdown
Quitting from lines 30-41 (geoms.Rmd) 
Error: processing vignette 'geoms.Rmd' failed with diagnostics:
invalid line type
--- failed re-building 'geoms.Rmd'

--- re-building 'gtable_show_lemonade.Rmd' using rmarkdown
Quitting from lines 42-61 (gtable_show_lemonade.Rmd) 
Error: processing vignette 'gtable_show_lemonade.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'gtable_show_lemonade.Rmd'

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

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

SUMMARY: processing the following files failed:
  'geoms.Rmd' 'gtable_show_lemonade.Rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/liayson.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      3.0Mb
Running 'testthat.R' [94s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > 
  > test_check("lidR")
  -- 1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalo
  projection(req2) not equal to "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clrk66 +units=m +no_defs".
  1/1 mismatches
  x[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  x[1]: k66 +units=m +no_defs "
  y[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  y[1]: k66 +units=m +no_defs"
  
  == testthat results  ===========================================================
  [ OK: 971 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalog_apply-automerge.R#171) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [82s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > 
  > test_check("lidR")
  -- 1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalo
  projection(req2) not equal to "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clrk66 +units=m +no_defs".
  1/1 mismatches
  x[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  x[1]: k66 +units=m +no_defs "
  y[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  y[1]: k66 +units=m +no_defs"
  
  == testthat results  ===========================================================
  [ OK: 971 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalog_apply-automerge.R#171) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   2.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.6Mb
    testdata   1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/lmQCM.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'logisticRR.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 162-169 (logisticRR.Rmd) 
Error: processing vignette 'logisticRR.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'logisticRR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: 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/4.0gcc8/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: 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/4.0gcc8/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: 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/4.0gcc8/lolog.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/LoopRig.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      2.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   3.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.1Mb
    libs   2.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   2.1Mb
Found the following significant warnings:
  liblwgeom/lwgeom_topo.c:4305:36: warning: too many arguments for format [-Wformat-extra-args]
  liblwgeom/lwgeom_topo.c:4357:38: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/lwgeom.Rcheck/00install.out' for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
    proj   5.0Mb
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/4.0gcc8/lxb.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:
> cleanEx()
> nameEx("interactive_threshold")
> ### * interactive_threshold
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: interactive_threshold
> ### Title: interactive thresholding
> ### Aliases: interactive_threshold
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1 0.09 1.11 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  34.7Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.2Mb
    htmlwidgets   1.8Mb
    libs          7.1Mb
Running examples in 'mapview-Ex.R' failed
The error most likely occurred in:

> ### Name: +
> ### Title: mapview + mapview adds data from the second map to the first
> ### Aliases: + +,mapview,mapview-method +,mapview,ANY-method
> ###   +,mapview,NULL-method +,mapview,character-method
> 
> ### ** Examples
> 
> m1 <- mapView(franconia, col.regions = "red")
> m2 <- mapView(breweries)
> 
> ### add two mapview objects
> m1 + m2
Error in if (!is.na(getProjection(lst[[i]]))) { : 
  argument is of length zero
Calls: + -> + -> combineExtent -> do.call -> lapply -> FUN
Execution halted
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mapview)
  > 
  > test_check("mapview")
  -- 1. Failure: getProjection() runs without issues (@test-mapviewControls.R#108)
  getProjection(franconia) has type `NULL`, not `character`.
  
  -- 2. Failure: getProjection() runs without issues (@test-mapviewControls.R#109)
  getProjection(franconia) not equal to "+proj=longlat +datum=WGS84 +no_defs".
  target is NULL, current is character
  
  == testthat results  ===========================================================
  [ OK: 63 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: getProjection() runs without issues (@test-mapviewControls.R#108) 
  2. Failure: getProjection() runs without issues (@test-mapviewControls.R#109) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mapview)
  > 
  > test_check("mapview")
  -- 1. Failure: getProjection() runs without issues (@test-mapviewControls.R#108)
  getProjection(franconia) has type `NULL`, not `character`.
  
  -- 2. Failure: getProjection() runs without issues (@test-mapviewControls.R#109)
  getProjection(franconia) not equal to "+proj=longlat +datum=WGS84 +no_defs".
  target is NULL, current is character
  
  == testthat results  ===========================================================
  [ OK: 63 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: getProjection() runs without issues (@test-mapviewControls.R#108) 
  2. Failure: getProjection() runs without issues (@test-mapviewControls.R#109) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   3.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.3Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mcmcabn.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      2.1Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   5.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Mega2R.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.6Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/metaboGSE.Rcheck/00install.out' for details.
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  -- 1. Error: Converting to phyloseq (@test--parsers_and_writers.R#202)  --------
  package or namespace load failed for 'phyloseq':
   .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
   1. base::library(phyloseq)
   2. base::tryCatch(...)
   3. base:::tryCatchList(expr, classes, parentenv, handlers)
   4. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5. value[[3L]](cond)
  
  == testthat results  ===========================================================
  [ OK: 95 | SKIPPED: 1 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Converting to phyloseq (@test--parsers_and_writers.R#202) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [26s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  -- 1. Error: Converting to phyloseq (@test--parsers_and_writers.R#202)  --------
  package or namespace load failed for 'phyloseq':
   .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
   1. base::library(phyloseq)
   2. base::tryCatch(...)
   3. base:::tryCatchList(expr, classes, parentenv, handlers)
   4. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5. value[[3L]](cond)
  
  == testthat results  ===========================================================
  [ OK: 95 | SKIPPED: 1 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Converting to phyloseq (@test--parsers_and_writers.R#202) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MetaPath.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/metap.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/metapro.Rcheck/00install.out' for details.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.4Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs   4.6Mb
    misc   1.1Mb
Error(s) in re-building vignettes:
--- re-building 'MfUSampler.Rnw' using Sweave
MfUSampler 1.0.4
Convenience Functions for Multivariate MCMC Using Univariate Samplers
For citations, please use:
Alireza S. Mahani, Mansour T. A. Sharabiani (2017). Multivariate-From-Univariate MCMC Sampler: The R Package MfUSampler. Journal of Statistical Software, Code Snippets, 78(1), 1-22. doi:10.18637/jss.v078.c01

Error: processing vignette 'MfUSampler.Rnw' failed with diagnostics:
 chunk 31 
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! D:/Compiler/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: fileb7b426ad39e5.o:fileb7b426ad39e5.cpp:(.text+0x4df): undefined reference to `dgemv_'
D:/Compiler/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: fileb7b426ad39e5.o:fileb7b426ad39e5.cpp:(.text+0x66f): undefined reference to `dgemv_'
collect2.exe: error: ld returned 1 exit status

--- failed re-building 'MfUSampler.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > #library(microsamplingDesign)
  > 
  > #source("generateTestData.R")
  > 
  > #test_check("microsamplingDesign")
  > 
  > testthat::test_check("microsamplingDesign")
  Loading required package: microsamplingDesign
  Loading required package: Rcpp
  start Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 cores-- 1. Failure: fastRank schemes , default fixed options identcal results  (@test
  all.equal(getRanking(origExample), getRanking(fastExample)) isn't true.
  
  -- 2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@t
  rankedSetOfSchemesOrig@ranking not equal to rankedSetOfSchemesNew@ranking.
  Component "name": 'current' is not a factor
  
  -- 3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47)  ------------
  rankTimePointsOrig@ranking not equal to rankedTimePointsNew@ranking.
  Component "name": 'current' is not a factor
  
  == testthat results  ===========================================================
  [ OK: 18 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: fastRank schemes , default fixed options identcal results  (@testRankSetOfSchemes.R#87) 
  2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@testRankSetOfSchemes.R#95) 
  3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [21s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > #library(microsamplingDesign)
  > 
  > #source("generateTestData.R")
  > 
  > #test_check("microsamplingDesign")
  > 
  > testthat::test_check("microsamplingDesign")
  Loading required package: microsamplingDesign
  Loading required package: Rcpp
  start Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 cores-- 1. Failure: fastRank schemes , default fixed options identcal results  (@test
  all.equal(getRanking(origExample), getRanking(fastExample)) isn't true.
  
  -- 2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@t
  rankedSetOfSchemesOrig@ranking not equal to rankedSetOfSchemesNew@ranking.
  Component "name": 'current' is not a factor
  
  -- 3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47)  ------------
  rankTimePointsOrig@ranking not equal to rankedTimePointsNew@ranking.
  Component "name": 'current' is not a factor
  
  == testthat results  ===========================================================
  [ OK: 18 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: fastRank schemes , default fixed options identcal results  (@testRankSetOfSchemes.R#87) 
  2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@testRankSetOfSchemes.R#95) 
  3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/miRtest.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mixKernel.Rcheck/00install.out' for details.
Running 'testthat.R' [128s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("checkmate")
  > library("testthat")
  > library("mlr3")
  > library("paradox")
  > library("mlr3pipelines")
  > 
  > test_check("mlr3pipelines")
  Training debug.multi with input list(input_1 = 1, input_2 = 1)
  -- 1. Error: LearnerClassifAvg (@test_learner_weightedaverage.R#12)  -----------
  <TaskClassif:tsk> has the following unsupported feature types: character
  Backtrace:
   1. lrn$train(tsk)
   2. mlr3::assert_learnable(task, self)
   3. mlr3misc::stopf(...)
  
  -- 2. Error: PipeOpRemoveConstants removes expected cols (@test_pipeop_removecon
  Target column 'target' must have at least two levels
  Backtrace:
   1. mlr3pipelines:::test_dropping(iris, iris, list())
   2. TaskClassif$new(...)
   3. .subset2(public_bind_env, "initialize")(...)
   4. private$.update_class_property()
   5. mlr3misc::stopf(...)
  
  == testthat results  ===========================================================
  [ OK: 7497 | SKIPPED: 44 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: LearnerClassifAvg (@test_learner_weightedaverage.R#12) 
  2. Error: PipeOpRemoveConstants removes expected cols (@test_pipeop_removeconstants.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MM2S.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   2.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.1Mb
Running 'testthat.R' [84s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > library("checkmate")
  > library("testthat")
  > library("ParamHelpers")
  > library("mlr")
  'mlr' is in maintenance mode since July 2019. Future development
  efforts will go into its successor 'mlr3' (<https://mlr3.mlr-org.com>).
  > library("mlrCPO")
  > 
  > test_check("mosmafs")
  Loading required package: mosmafs
  Loading required package: ecr
  Loading required package: BBmisc
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  Loading required package: smoof
  
  Attaching package: 'ecr'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  
  Attaching package: 'mosmafs'
  
  The following objects are masked from 'package:ecr':
  
      getPopulations, getStatistics
  
  -- 1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232)  ---------
  `slickEcr(...)` threw an error with unexpected message.
  Expected match: "Must be of type 'numeric', not 'factor'"
  Actual message: "Assertion on 'fidelity[[2]]' failed: Must be of type 'numeric', not 'character'."
  Backtrace:
    1. testthat::expect_error(...)
    6. mosmafs::slickEcr(...)
    7. mosmafs::initEcr(...)
    8. mosmafs:::checkFidelity(fidelity)
    9. checkmate::assertNumeric(fidelity[[2]], any.missing = FALSE)
   10. checkmate::makeAssertion(x, res, .var.name, add)
   11. checkmate:::mstop(...)
  
  == testthat results  ===========================================================
  [ OK: 458 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   1.9Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    libs         14.0Mb
    mathematica   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MRPC.Rcheck/00install.out' for details.
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  21.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MSIseq.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/msSurv.Rcheck/00install.out' for details.
Running examples in 'MST-Ex.R' failed
The error most likely occurred in:

> ### Name: MST
> ### Title: Multivariate Survival Trees
> ### Aliases: MST splitting.stat.MST1 splitting.stat.MST2
> ###   splitting.stat.MST3 splitting.stat.MST4
> ### Keywords: Trees Survival Multivariate Correlated
> 
> ### ** Examples
> 
> set.seed(186117)
> data <- rmultime(N = 200, K = 4, beta = c(-1, 0.8, 0.8, 0, 0), cutoff = c(0.5, 0.3, 0, 0),
+     model = "marginal.multivariate.exponential", rho = 0.65)$dat
> test <- rmultime(N = 100, K = 4, beta = c(-1, 0.8, 0.8, 0, 0), cutoff = c(0.5, 0.3, 0, 0),
+     model = "marginal.multivariate.exponential", rho = 0.65)$dat
> 
> #Construct Multivariate Survival Tree:
> fit <- MST(formula = Surv(time, status) ~ x1 + x2 + x3 + x4 | id, data, test,
+     method = "marginal", minsplit = 100, minevents = 20, selection.method = "test.sample")
Error in plot.window(...) : need finite 'ylim' values
Calls: MST -> plot -> plot.default -> localWindow -> plot.window
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/multicross.Rcheck/00install.out' for details.
Found the following significant warnings:
  eclat/tract/src/tract.c:1399:41: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/multinet.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mutossGUI.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mutoss.Rcheck/00install.out' for details.
plot.matchedwake: no visible global function definition for
  'filled.contour'
plot.matchedwake: no visible binding for global variable 'gray.colors'
plot.matchedwake: no visible global function definition for 'axis'
plot.matchedwake: no visible global function definition for 'rect'
slideWakeMatch: no visible binding for global variable 'lm'
slideWakeMatch: no visible global function definition for 'as.formula'
slideWakeMatch: no visible global function definition for 'summary.glm'
Undefined global functions or variables:
  as.formula axis filled.contour gray.colors lm rect summary.glm
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "axis", "filled.contour", "rect")
  importFrom("stats", "as.formula", "lm", "summary.glm")
to your NAMESPACE file.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
    libs   2.0Mb
Running examples in 'nandb-Ex.R' failed
The error most likely occurred in:

> ### Name: brightness
> ### Title: Calculate brightness from image series.
> ### Aliases: brightness
> 
> ### ** Examples
> 
> img <- ijtiff::read_tif(system.file("extdata", "50.tif", package = "nandb"))
Running 'spelling.R' [0s]
  Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(nandb)
  > 
  > test_check("nandb")
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/4.0gcc8/NestedCategBayesImpute.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/netgsa.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.6Mb
Packages in Depends field not imported from:
  'MASS' 'boot' 'lattice' 'psych'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in 'nFactors-Ex.R' failed
The error most likely occurred in:

> ### Name: eigenComputes
> ### Title: Computes Eigenvalues According to the Data Type
> ### Aliases: eigenComputes
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> # .......................................................
> # Different data types
> # Vector of eigenvalues
>   data(dFactors)
>   x1 <- dFactors$Cliff1$eigenvalues
>   eigenComputes(x1)
 [1]  2.842  1.080  0.640  0.171  0.015 -0.008 -0.008 -0.126 -0.040 -0.066
[11] -0.111 -0.116
>   
> # Data from a data.frame
>   x2 <- data.frame(matrix(20*rnorm(100), ncol=5))
>   eigenComputes(x2, cor=TRUE,  use="everything")
[1] 1.5562290 1.3713228 1.1323986 0.6806224 0.2594272
>   eigenComputes(x2, cor=FALSE, use="everything")
[1] 527.95290 485.38169 365.44540 209.02148  84.80241
>   eigenComputes(x2, cor=TRUE,  use="everything", method="spearman")
[1] 1.486597 1.448541 1.249002 0.625795 0.190065
>   eigenComputes(x2, cor=TRUE,  use="everything", method="kendall")
[1] 1.3682956 1.3334477 1.2159607 0.7120364 0.3702597
> 
> # From a covariance matrix
>   x3 <- cov(x2)
>   eigenComputes(x3, cor=TRUE,  use="everything")
Error in switch(classType, data.frame = "data", matrix = "correlation",  : 
  EXPR must be a length 1 vector
Calls: eigenComputes -> eigenFrom
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    CppCode   2.7Mb
    R         6.1Mb
    include   5.6Mb
    libs      2.4Mb
    tests     1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/NIPTeR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/nlcv.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs   3.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.2Mb
Found the following significant warnings:
  Warning: replacing previous import 'sf::st_make_valid' by 'lwgeom::st_make_valid' when loading 'oceanis'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/oceanis.Rcheck/00install.out' for details.
Running examples in 'oceanis-Ex.R' failed
The error most likely occurred in:

> ### Name: coordonnees_etiquettes
> ### Title: Data table of labels
> ### Aliases: coordonnees_etiquettes
> ### Keywords: documentation
> 
> ### ** Examples
> 
> data("donnees_monoloc")
> data("depm")
> 
> etiquettes <- coordonnees_etiquettes(fondMaille = depm,
+ listeCode = c("06","13","31","33","44","67","69","59","75"))
> etiquettes$LIBELLE <- c("Nice","Marseille","Toulouse","Bordeaux","Nantes",
+ "Lille","Strasbourg","Lyon","Paris")
> etiquettes[etiquettes$CODE=="75","TAILLE"] <- 1.3
> 
> # Ronds proportionnels sur une analyse en classes
> fond_ronds <- plot_classes_ronds(data = donnees_monoloc, fondMaille = depm,
+ idData = "COD_DEP", varVolume = "POP_2015", varRatio = "VAR_AN_MOY", nbClasses = 4,
+ titreLegRonds = "POP_2015", titreLegClasses = "VAR_AN_MOY",
+ xLegClasses = 1150000, yLegClasses = 6600000, etiquettes = etiquettes)
Warning in CPL_crs_from_input(x) :
  GDAL Error 6: EPSG PCS/GCS code 0 not found in EPSG support files.  Is this a valid EPSG coordinate system?
Error in CPL_transform(x, crs, aoi, pipeline, reverse) : 
  crs not found: is it missing?
Calls: plot_classes_ronds ... st_transform -> st_transform.sfc -> structure -> CPL_transform
Execution halted
Error(s) in re-building vignettes:
--- re-building 'integration_shiny.Rmd' using rmarkdown
--- finished re-building 'integration_shiny.Rmd'

--- re-building 'oceanis.Rmd' using rmarkdown
Quitting from lines 118-179 (oceanis.Rmd) 
Error: processing vignette 'oceanis.Rmd' failed with diagnostics:
st_crs(x) == st_crs(y) is not TRUE
--- failed re-building 'oceanis.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.3Mb
    help   2.7Mb
    libs   2.5Mb
Running examples in 'ODEnetwork-Ex.R' failed
The error most likely occurred in:

> ### Name: setEvents
> ### Title: Setting Events
> ### Aliases: setEvents
> 
> ### ** Examples
> 
> masses <- 1
> dampers <- as.matrix(1.5)
> springs <- as.matrix(4)
> odenet <- ODEnetwork(masses, dampers, springs)
> eventdat <- data.frame(  var = c("x.1", "x.1")
+                        , time = c(1, 3)
+                        , value = c(1, 3)
+                        )
> odenet <- setState(odenet, 0, 0)
> odenet <- setEvents(odenet, eventdat)
Error: Assertion failed. One of the following must apply:
 * checkDataFrame(events): May only contain the following types:
 * {factor,numeric,numeric}, but element 1 has type 'character'
 * checkDataFrame(events): Must have exactly 4 cols, but has 3 cols
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ODEnetwork.Rmd' using rmarkdown
Quitting from lines 168-175 (ODEnetwork.Rmd) 
Error: processing vignette 'ODEnetwork.Rmd' failed with diagnostics:
Assertion failed. One of the following must apply:
 * checkDataFrame(events): May only contain the following types:
 * {factor,numeric,numeric}, but element 1 has type 'character'
 * checkDataFrame(events): Must have exactly 4 cols, but has 3 cols
--- failed re-building 'ODEnetwork.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/omu.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.4Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ontologyPlot.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/OpenCL.Rcheck/00install.out' for details.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs   19.8Mb
    share   9.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.9Mb
    models   4.6Mb
Running 'testthat.R' [41s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(OpenMx)
  > 
  > test_check("OpenMx")
  -- 1. Failure: (unknown) (@test-wls-binary.R#43)  ------------------------------
  `mxRun(wlsTest4)` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 567 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: (unknown) (@test-wls-binary.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/orQA.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    doc    1.3Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/PANDA.Rcheck/00install.out' for details.
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/4.0gcc8/pbdRPC.Rcheck/00install.out' for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.5Mb
    libs   4.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  13.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/PCGSE.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/PCS.Rcheck/00install.out' for details.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs   13.8Mb
    share  11.9Mb
Running 'script.R' [1s]
  Running 'testthat.R' [3s]
Running the tests in 'tests/script.R' failed.
Complete output:
  > ## I initially tried writing these tests using testthat, but I got
  > ## errors when using the system() and system2() functions (bug in
  > ## testthat).
  > PeakError_compute.R <- system.file(
  +   "exampleData", "PeakError_compute.R",
  +   mustWork=TRUE,
  +   package="PeakError")
  > Rscript <- R.home(file.path("bin", "Rscript"))
  > exampleData <- system.file("exampleData", package="PeakError", mustWork=TRUE)
  > peaks.bed <- file.path(exampleData, "peaks.bed")
  > labels.bed <- file.path(exampleData, "labels.bed")
  > overlapping.bed <- file.path(exampleData, "overlapping_peaks.bed")
  > 
  > ##test_that("PeakError_compute.R correct", {
  > out.file <- tempfile()
  > cmd <- paste(Rscript, PeakError_compute.R, peaks.bed, labels.bed, ">", out.file)
  > status <- system(cmd)
  Error: Usage: compute_error.R peaks.bed labels.bed > errors.bed
  Execution halted
  > errors <- read.table(out.file, sep="\t", header=TRUE)
  Error in file(file, "rt") : cannot open the connection
  Calls: read.table -> file
  In addition: Warning message:
  In file(file, "rt") :
    cannot open file 'D:\temp\Rtmpwdg80K\filef7886ecd4656': No such file or directory
  Execution halted
Running 'script.R' [1s]
  Running 'testthat.R' [3s]
Running the tests in 'tests/script.R' failed.
Complete output:
  > ## I initially tried writing these tests using testthat, but I got
  > ## errors when using the system() and system2() functions (bug in
  > ## testthat).
  > PeakError_compute.R <- system.file(
  +   "exampleData", "PeakError_compute.R",
  +   mustWork=TRUE,
  +   package="PeakError")
  > Rscript <- R.home(file.path("bin", "Rscript"))
  > exampleData <- system.file("exampleData", package="PeakError", mustWork=TRUE)
  > peaks.bed <- file.path(exampleData, "peaks.bed")
  > labels.bed <- file.path(exampleData, "labels.bed")
  > overlapping.bed <- file.path(exampleData, "overlapping_peaks.bed")
  > 
  > ##test_that("PeakError_compute.R correct", {
  > out.file <- tempfile()
  > cmd <- paste(Rscript, PeakError_compute.R, peaks.bed, labels.bed, ">", out.file)
  > status <- system(cmd)
  Error: Usage: compute_error.R peaks.bed labels.bed > errors.bed
  Execution halted
  > errors <- read.table(out.file, sep="\t", header=TRUE)
  Error in file(file, "rt") : cannot open the connection
  Calls: read.table -> file
  In addition: Warning message:
  In file(file, "rt") :
    cannot open file 'D:\temp\Rtmpua1Y1p\file2c8482559430f': No such file or directory
  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:11388 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11388 (sockconn)
Execution halted
create.data: no visible global function definition for 'rexp'
create.data: no visible global function definition for 'runif'
create.data: no visible global function definition for 'rbinom'
opt.splitval: no visible global function definition for 'na.omit'
opt2D : opt.both: no visible global function definition for 'optim'
Undefined global functions or variables:
  na.omit optim rbinom rexp runif
Consider adding
  importFrom("stats", "na.omit", "optim", "rbinom", "rexp", "runif")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs        2.0Mb
    xvg-files   3.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/phateR.Rcheck/00install.out' for details.
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Content type 'application/octet-stream' length 205186 bytes (200 KB)
  ==================================================
  downloaded 200 KB
  
  -- 1. Failure: test getting awb data (@testphenocamapi.R#42)  ------------------
  `wb` not equal to "LIKELY_NO".
  target is NULL, current is character
  
  == testthat results  ===========================================================
  [ OK: 5 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: test getting awb data (@testphenocamapi.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_phenocam_api.Rmd' using rmarkdown
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 205186 bytes (200 KB)
==================================================
downloaded 200 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/2013/05/dukehw_2013_05_31_150331.jpg'
Content type 'image/jpeg' length 470270 bytes (459 KB)
==================================================
downloaded 459 KB

Quitting from lines 282-298 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
a character vector argument expected
--- failed re-building 'getting_started_phenocam_api.Rmd'

--- re-building 'phenocam_data_fusion.Rmd' using rmarkdown
Loading required package: rjson
Loading required package: RCurl
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 205186 bytes (200 KB)
==================================================
downloaded 200 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/oregonMP/ROI/oregonMP_EN_1000_3day.csv'
Content type 'application/octet-stream' length 271209 bytes (264 KB)
==================================================
downloaded 264 KB

--- finished re-building 'phenocam_data_fusion.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.0Mb
    libs      2.0Mb
Found the following apparent S3 methods exported but not registered:
  cospi.generic_spct sinpi.generic_spct tanpi.generic_spct
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
S3 methods shown with full name in documentation object 'Trig':
  'cospi.generic_spct' 'sinpi.generic_spct' 'tanpi.generic_spct'

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  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/phyloseqGraphTest.Rcheck/00install.out' for details.
Warning in inla.print.version() :
  INLA_18.07.12: 32bit binaries are no longer supported!

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.
Running 'test-async.R' [19s]
  Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pkgcache)
  > 
  > test_check("pkgcache")
  -- 1. Error: load_primary_pkgs (@test-metadata-cache.R#191)  -------------------
  No metadata available
  Backtrace:
   1. pkgcache:::synchronise(get_private(cmc)$load_primary_pkgs(oneday()))
   2. get_private(cmc)$load_primary_pkgs(oneday())
   3. pkgcache:::cmc__load_primary_pkgs(self, private, max_age)
   4. private$update_replica_rds(alert = FALSE)
   5. pkgcache:::cmc__update_replica_rds(self, private, alert)
  
  == testthat results  ===========================================================
  [ OK: 305 | SKIPPED: 28 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: load_primary_pkgs (@test-metadata-cache.R#191) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'PK-Ex.R' failed
The error most likely occurred in:

> ### Name: nca
> ### Title: Estimation of various PK parameters
> ### Aliases: nca nca.ssd nca.batch nca.complete
> ### Keywords: htest
> 
> ### ** Examples
> 
> #### serial sampling designs
> ## example for a serial sampling data design from Wolfsegger and Jaki (2009)
> conc <- c(0, 0, 0, 2.01, 2.85, 2.43, 0.85, 1.00, 0.91, 0.46, 0.35, 0.63, 0.39, 0.32, 
+           0.45, 0.11, 0.18, 0.19, 0.08, 0.09, 0.06)
> time <- c(rep(0,3), rep(5/60,3), rep(3,3), rep(6,3), rep(9,3), rep(16,3), rep(24,3))
> 
> # Direct call of the function
> # CAUTION: this might take a few minutes
> # Note: 1E4 bootstrap replications were used in the example given 
> # in Wolfsegger and Jaki (2009)
> set.seed(34534)
> nca.ssd(conc=conc, time=time, n.tail=4, dose=200, method=c("z","boott"), 
+          conf.level=0.95, nsample=500)
Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
Calls: nca.ssd ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<-
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/PlasmaMutationDetector.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.6Mb
Running 'testthat.R' [102s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("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
  
  > 
  > test_check("plotly")
  Visual testing is not enabled.
  OGR: Unsupported geometry type
  -- 1. Error: (unknown) (@test-cookbook-lines.R#192)  ---------------------------
  arguments imply differing number of rows: 0, 2
  Backtrace:
   1. base::data.frame(cond = levels(df$cond), xval = c(10, 11.5))
  
  -- 2. Failure: paths with the same color but different groups stay together (@te
  info$data[[1]]$name not identical to "positive".
  1/1 mismatches
  x[1]: "negative"
  y[1]: "positive"
  
  -- 3. Failure: paths with the same color but different groups stay together (@te
  info$data[[2]]$name not identical to "negative".
  1/1 mismatches
  x[1]: "positive"
  y[1]: "negative"
  
  == testthat results  ===========================================================
  [ OK: 1375 | SKIPPED: 50 | WARNINGS: 63 | FAILED: 3 ]
  1. Error: (unknown) (@test-cookbook-lines.R#192) 
  2. Failure: paths with the same color but different groups stay together (@test-ggplot-path.R#51) 
  3. Failure: paths with the same color but different groups stay together (@test-ggplot-path.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: 'gt'
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(polite)
  > 
  > test_check("polite")
  -- 1. Error: Bow warns about disallowed url (@test_bow.R#5)  -------------------
  SSL certificate problem: unable to get local issuer certificate
  Backtrace:
    1. testthat::expect_warning(...)
    6. polite::bow("https://www.wikipedia.org/w/", verbose = TRUE)
    7. robotstxt::robotstxt(...)
    8. robotstxt::get_robotstxt(...)
    9. robotstxt:::get_robotstxt_http_get(...)
   10. httr::GET(...)
   11. httr:::request_perform(req, hu$handle$handle)
   13. httr:::request_fetch.write_memory(req$output, req$url, handle)
   14. curl::curl_fetch_memory(url, handle = handle)
  
  -- 2. Error: Nod warns about disallowed url (@test_nod.R#5)  -------------------
  SSL certificate problem: unable to get local issuer certificate
  Backtrace:
    1. testthat::expect_warning(...)
    7. polite::bow("https://www.wikipedia.org/")
    8. robotstxt::robotstxt(...)
    9. robotstxt::get_robotstxt(...)
   10. robotstxt:::get_robotstxt_http_get(...)
   11. httr::GET(...)
   12. httr:::request_perform(req, hu$handle$handle)
   14. httr:::request_fetch.write_memory(req$output, req$url, handle)
   15. curl::curl_fetch_memory(url, handle = handle)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: Bow warns about disallowed url (@test_bow.R#5) 
  2. Error: Nod warns about disallowed url (@test_nod.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.1Mb
    libs   2.3Mb
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/PPRL.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/pRF.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/prioGene.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ProbeDeveloper.Rcheck/00install.out' for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      2.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.1Mb
Running 'run-all.R' [32s]
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("ProjectTemplate")
  Loading required package: ProjectTemplate
  -- 1. Failure: Custom configuration is added to config (@test-add_config.R#12)  
  `load.project()` generated warnings:
  * 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
  
  v |  OK F W S | Context
  
  / |   0       | Example tests
  v |   1       | Example tests
  
  == Results =====================================================================
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  v |  OK F W S | Context
  
  / |   0       | Example tests
  v |   1       | Example tests
  
  == Results =====================================================================
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  
  You are a coding rockstar!
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] TRUE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  == testthat results  ===========================================================
  [ OK: 852 | SKIPPED: 4 | WARNINGS: 281 | FAILED: 1 ]
  1. Failure: Custom configuration is added to config (@test-add_config.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
    proj   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    libs   2.3Mb
Running examples in 'PROSPER-Ex.R' failed
The error most likely occurred in:

> ### Name: gen_diploid
> ### Title: Diploid genetics: recombination of alleles
> ### Aliases: gen_diploid
> 
> ### ** Examples
> 
> # generate a 'dfgenotype' data.frame:
> struc_preparation(Rmx=10, n_loci=2, epis=0, dom=1)
struc_preparation starts...Error in matrix(ncol = n_loci, as.numeric(unlist(strsplit(as.character(dfgenotype[,  : 
  invalid 'ncol' value (too large or NA)
Calls: struc_preparation -> sel_resist -> data.frame -> matrix
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/psSubpathway.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'barebones_correlation.Rmd' using rmarkdown
--- finished re-building 'barebones_correlation.Rmd'

--- re-building 'overview.Rmd' using rmarkdown
Quitting from lines 97-103 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
invalid 'row.names' length
--- failed re-building 'overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc        4.1Mb
    examples   2.6Mb
Running examples in 'PTXQC-Ex.R' failed
The error most likely occurred in:

> ### Name: plot_CalibratedMSErr
> ### Title: Plot bargraph of uncalibrated mass errors for each Raw file.
> ### Aliases: plot_CalibratedMSErr
> 
> ### ** Examples
> 
>   n = c(150, 1000, 1000, 1000)
>   data = data.frame(fc.raw.file = repEach(letters[4:1], n),
+                     mass.error..ppm. = c(rnorm(n[1], 1, 2.4),
+                                          rnorm(n[2], 0.5, 0.5),
+                                          rnorm(n[3], 0.1, 0.7),
+                                          rnorm(n[4], 0.3, 0.8)))
>   stats = data.frame(fc.raw.file = letters[4:1],
+                      sd = c(2.4, 0.5, 0.7, 0.8),
+                      outOfCal = c(TRUE, FALSE, FALSE, FALSE))           
>   plot_CalibratedMSErr(data, MQBug_raw_files = letters[1], stats, y_lim = c(-20,20), 15, "subtitle")
Error in scale_x_discrete_reverse(data$fc.raw.file) : 
  Cannot use scale_x_discrete_reverse() on non-factor()
Calls: plot_CalibratedMSErr -> scale_x_discrete_reverse
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/pulseTD.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.6Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   2.1Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rags2ridges.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ragt2ridges.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   3.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RAPIDR.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   2.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   4.3Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rblpapi.Rcheck/00install.out' for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RcmdrPlugin.BiclustGUI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rcplex.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   6.2Mb
    libs      2.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      2.4Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.9Mb
    libs      3.4Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      2.3Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      13.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.4Mb
    libs      2.5Mb
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(RcppXsimd)
  > 
  > test_check("RcppXsimd")
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcrypt)
  > 
  > test_check("rcrypt")
  gpg: decryption failed: bad key
  -- 1. Error: Decryption with passphrase passthrough and armor works (@test-decry
  cannot open the connection
  Backtrace:
   1. base::readLines("file2-decrypt.txt")
   2. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 18 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: Decryption with passphrase passthrough and armor works (@test-decrypt.r#69) 
  
  Error: testthat unit tests failed
  Execution halted
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/4.0gcc8/RDieHarder.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   2.3Mb
Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(renv)
  
  Attaching package: 'renv'
  
  The following object is masked from 'package:stats':
  
      update
  
  The following objects are masked from 'package:utils':
  
      history, upgrade
  
  The following objects are masked from 'package:base':
  
      load, remove
  
  > 
  > renv:::renv_tests_init()
  > renv:::renv_tests_diagnostics()
  The following R libraries are set:
  
  	- D:/temp/RtmpYXR0w2/renv-library-10e3c15d06db2
  	- D:/temp/RtmpYXR0w2/renv-system-library
  
  The following repositories are set:
  
  	CRAN: file:///D:\temp\RtmpYXR0w2\renv-repos-10e3c7d7517b2
  
  The following renv root directory is being used:
  
  	- D:\temp\RtmpYXR0w2\renv-root-10e3c252d56cf
  
  The following renv cache directory is being used:
  
  	- D:\temp\RtmpYXR0w2\renv-root-10e3c252d56cf/cache/v5/R-4.0/x86_64-w64-mingw32
  
  The following packages are available in the test repositories:
  
  	bread, breakfast, brunch, egg, halloween, oatmeal, packrat,
  	toast
  
  	R_LIBS      : <NA>
  	R_LIBS_SITE : "'no_such_dir'"
  	R_LIBS_USER : "'no_such_dir'"
  
  > 
  > test_check("renv")
  [4/4] -- 1. Error: we can retrieve files using file URIs (@test-retrieve.R#282)  -----
  (converted from warning) cannot open file 'D:/temp/RtmpYXR0w2/renv-test-10e3c5f746d5d/target': No such file or directory
  Backtrace:
   1. testthat::expect_equal(readLines(target), "Hello, world!")
   4. base::readLines(target)
  
  == testthat results  ===========================================================
  [ OK: 304 | SKIPPED: 53 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: we can retrieve files using file URIs (@test-retrieve.R#282) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.1Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(reshape2)
  > 
  > test_check("reshape2")
  -- 1. Failure: labels are correct when missing combinations dropped/kept (@test-
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 4 - 16 == -12
  
  == testthat results  ===========================================================
  [ OK: 126 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: labels are correct when missing combinations dropped/kept (@test-cast.r#126) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/restfulr.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs      2.5Mb
    swagger   1.4Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("retistruct")
  Loading required package: retistruct
  -- 1. Error: IDT format is read correctly (@test-format-idt.R#9)  --------------
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(r)
  
  -- 2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8)  -----------
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  -- 3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45)  
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  -- 4. Error: Serialisation works with a particular example (@test-reconstruct.R#
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a, error = message)
  
  -- 5. Error: No regression on Issue #21 (@test-regressions.R#5)  ---------------
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a)
  
  == testthat results  ===========================================================
  [ OK: 138 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 5 ]
  1. Error: IDT format is read correctly (@test-format-idt.R#9) 
  2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8) 
  3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45) 
  4. Error: Serialisation works with a particular example (@test-reconstruct.R#98) 
  5. Error: No regression on Issue #21 (@test-regressions.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("retistruct")
  Loading required package: retistruct
  -- 1. Error: IDT format is read correctly (@test-format-idt.R#9)  --------------
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(r)
  
  -- 2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8)  -----------
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  -- 3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45)  
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  -- 4. Error: Serialisation works with a particular example (@test-reconstruct.R#
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a, error = message)
  
  -- 5. Error: No regression on Issue #21 (@test-regressions.R#5)  ---------------
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a)
  
  == testthat results  ===========================================================
  [ OK: 138 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 5 ]
  1. Error: IDT format is read correctly (@test-format-idt.R#9) 
  2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8) 
  3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45) 
  4. Error: Serialisation works with a particular example (@test-reconstruct.R#98) 
  5. Error: No regression on Issue #21 (@test-regressions.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Error(s) in re-building vignettes:
--- re-building 'RFmerge-RainfallExample-minimal.Rmd' using rmarkdown

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Loading required package: sp
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: D:/temp/Rtmpkdw5Mi/RLIBS_240f4522736dc/rgdal/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: D:/temp/Rtmpkdw5Mi/RLIBS_240f4522736dc/rgdal/proj
 Linking to sp version: 1.4-1 
(C) 2019 M. Zambrano-Bigiarini and Oscar M. Baez-Villanueva (GPL >=3 license)
Type 'citation('RFmerge')' to see how to cite this package
Quitting from lines 268-274 (RFmerge-RainfallExample-minimal.Rmd) 
Error: processing vignette 'RFmerge-RainfallExample-minimal.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'RFmerge-RainfallExample-minimal.Rmd'

SUMMARY: processing the following file failed:
  'RFmerge-RainfallExample-minimal.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.4Mb
    extdata   1.9Mb
installed size is 80.9Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      69.2Mb
    pictures   1.3Mb
    proj       5.0Mb
Found the following significant warnings:
  IP2Location.c:339:35: warning: passing argument 3 of 'inet_pton' from incompatible pointer type [-Wincompatible-pointer-types]
  IP2Location.c:893:39: warning: passing argument 3 of 'inet_pton' from incompatible pointer type [-Wincompatible-pointer-types]
  IP2Location.c:900:41: warning: passing argument 3 of 'inet_pton' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rgeolocate.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      2.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.5Mb
    libs    1.4Mb
Packages suggested but not available for checking:
  'playwith', 'pmg', 'SVGAnnotation'
Found the following significant warnings:
  Note: possible error in 'coord_trans(xtrans = "exp", ': unused arguments (xtrans = "exp", ytrans = "exp") 
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RGraphics.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
figure5.11: possible error in coord_trans(xtrans = "exp", ytrans =
  "exp"): unused arguments (xtrans = "exp", ytrans = "exp")
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.7Mb
    libs   5.1Mb
Found the following significant warnings:
  fakemaster.c:82:57: warning: embedded '\0' in format [-Wformat-contains-nul]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rhpc.Rcheck/00install.out' for details.
Found the following significant warnings:
  chemutil.c:339:23: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ribiosUtils.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RichR.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/4.0gcc8/RInside.Rcheck/00install.out' for details.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    lib    6.6Mb
    libs   8.1Mb
Running examples in 'RISCA-Ex.R' failed
The error most likely occurred in:

> ### Name: expect.utility2
> ### Title: Cut-Off Estimation Of A Prognostic Marker (Two Groups Are
> ###   observed).
> ### Aliases: expect.utility2
> ### Keywords: Utility
> 
> ### ** Examples
> 
> 
> # import and attach the data example
> 
> data(dataCSL)
> dataCSL <- dataCSL[order(dataCSL$id, dataCSL$time),]
> dataCSL$ordre <-0
> for (i in unique(dataCSL$id))
+  {dataCSL$ordre[dataCSL$id==i] <- 1:sum(dataCSL$id==i)}
> 
> dataCSL$ttt[dataCSL$treat==0]<-"A"
> dataCSL$ttt[dataCSL$treat==1]<-"B"
> 
> dataCSL0 <- dataCSL[dataCSL$ordre==1,]
> dataCSL0<-dataCSL0[,c(1,4,5,14,9)]
> 
> # the expected utility function for a prognostic up to 8 years
> 
> EUt.obj <- expect.utility2(dataCSL0$eventT, dataCSL0$dc,
+  dataCSL0$prot.base, treatment= dataCSL0$ttt,
+  pro.time=8, u.A0=0.75*0.95, u.A1=0, u.B0=0.75, u.B1=0)
Warning in expect.utility2(dataCSL0$eventT, dataCSL0$dc, dataCSL0$prot.base,  :
  NAs introduced by coercion
Warning in max(tab.res$utility, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(tab.res$utility, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(event[who2]) :
  no non-missing arguments to max; returning -Inf
Error in rep(1:nstrat, x$strata) : invalid 'times' argument
Calls: expect.utility2 -> meanALL -> summary -> summary.survfit -> survmean
Execution halted
Found the following significant warnings:
  Rinit.c:251:21: warning: assignment to 'blah1' {aka 'int (*)(const char *, char *, int,  int)'} from incompatible pointer type 'int (*)(const char *, unsigned char *, int,  int)' [-Wincompatible-pointer-types]
  Rinit.c:257:21: warning: assignment to 'blah5' {aka 'int (*)(const char *)'} from incompatible pointer type 'int (*)(char *)' [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rJava.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/4.0gcc8/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/4.0gcc8/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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.
Running examples in 'Rlabkey-Ex.R' failed
The error most likely occurred in:

> ### Name: getFolderPath
> ### Title: Returns the folder path associated with a session
> ### Aliases: getFolderPath
> ### Keywords: file
> 
> ### ** Examples
> 
> 
> # library(Rlabkey)
> 
> lks<- getSession("http://www.labkey.org", "/home")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: unable to get local issuer certificate
Calls: getSession ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rmagic.Rcheck/00install.out' for details.
Running 'testthat.R' [61s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("rmapshaper")
  > 
  > test_check("rmapshaper")
  -- 1. Failure: NA values dealt with in sf_to_GeoJSON (@test-utils.R#58)  -------
  `geojson` not equal to structure(...).
  Attributes: < Component "proj4": Names: 2 string mismatches >
  Attributes: < Component "proj4": Component 1: Modes: character, numeric >
  Attributes: < Component "proj4": Component 1: target is character, current is numeric >
  
  == testthat results  ===========================================================
  [ OK: 292 | SKIPPED: 30 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: NA values dealt with in sf_to_GeoJSON (@test-utils.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rmRNAseq.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doxygen   1.4Mb
    libs      2.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      6.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RobLoxBioC.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'using_robotstxt.Rmd' using rmarkdown

 google.com                      Quitting from lines 48-51 (using_robotstxt.Rmd) 
Error: processing vignette 'using_robotstxt.Rmd' failed with diagnostics:
SSL certificate problem: unable to get local issuer certificate
--- failed re-building 'using_robotstxt.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ROracle.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs    2.2Mb
    tests   1.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.5Mb
Found the following significant warnings:
  fe-protocol2.c:1615:2: warning: 'strncpy' specified bound 32 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1616:2: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1620:3: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RPostgreSQL.Rcheck/00install.out' for details.
Running examples in 'Rprofet-Ex.R' failed
The error most likely occurred in:

> ### Name: ScorecardProfet
> ### Title: Scorecard Builder
> ### Aliases: ScorecardProfet
> 
> ### ** Examples
> 
> mydata <- ISLR::Default
> 
> mydata$ID = seq(1:nrow(mydata)) ## make the ID variable
> mydata$default<-ifelse(mydata$default=="Yes",1,0) ## Creating numeric binary target variable
> 
> binned <- BinProfet(mydata, id= "ID", target= "default", num.bins = 5) ## Binning variables
> 
> WOE_dat <- WOEProfet(binned, "ID","default", 3:5) ## WOE transformation of bins
Error in aggregate.data.frame(lhs, mf[-1L], FUN = FUN, ...) : 
  no rows to aggregate
Calls: WOEProfet ... aggregate -> aggregate.formula -> aggregate.data.frame
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
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/4.0gcc8/RSclient.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RSeed.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/4.0gcc8/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/4.0gcc8/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/4.0gcc8/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/4.0gcc8/RSNNS.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rsolr.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.4Mb
    libs  17.5Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rstap.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.6Mb
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 alpha (2020-03-26 r78078)
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()
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.3Mb
    projects   2.7Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   5.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.8Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      8.9Mb
Error(s) in re-building vignettes:
--- re-building 'rxnat.Rmd' using rmarkdown
Quitting from lines 98-100 (rxnat.Rmd) 
Error: processing vignette 'rxnat.Rmd' failed with diagnostics:
error during HTTP request
--- failed re-building 'rxnat.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Running 'testthat.R' [57s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(RxODE)
  > test_check("RxODE")
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 44-46 (sentiment.Rmd) 
Error: processing vignette 'sentiment.Rmd' failed with diagnostics:
SSL certificate problem: unable to get local issuer certificate
--- failed re-building 'sentiment.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   2.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    extdata   1.3Mb
    libs      2.0Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/scmamp.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/scMappR.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   2.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SeqFeatR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SeqGrapheR.Rcheck/00install.out' for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/seqmagick.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/sequenza.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Seurat.Rcheck/00install.out' for details.
installed size is 95.8Mb
  sub-directories of 1Mb or more:
    doc     11.9Mb
    gdal     3.9Mb
    libs    70.7Mb
    proj     5.0Mb
    sqlite   1.5Mb
Error(s) in re-building vignettes:
--- re-building 'sigminer.Rmd' using rmarkdown
Quitting from lines 68-72 (sigminer.Rmd) 
Error: processing vignette 'sigminer.Rmd' failed with diagnostics:
package 'S4Vectors' could not be loaded
--- failed re-building 'sigminer.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Signac.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SIGN.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SigTree.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SimRAD.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SimReg.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.1Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(slga)
  > 
  > test_check("slga")
  -- 1. Error: validate_aoi functions as expected  -------------------------------
  st_crs(x) == st_crs(y) is not TRUE
  Backtrace:
   1. slga:::validate_aoi(bne_surface_clay, "NAT")
   2. slga:::aoi_overlaps(ext, product)
   6. sf:::st_intersects.sfc(sf::st_as_sfc(aoi), sf::st_as_sfc(prd_aoi))
   7. sf:::st_geos_binop("intersects", x, y, sparse = sparse, prepared = prepared)
   8. base::stopifnot(st_crs(x) == st_crs(y))
  
  == testthat results  ===========================================================
  [ OK: 140 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: validate_aoi functions as expected 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/smapr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SmartSVA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SMITIDstruct.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.1Mb
Running 'testthat.R' [91s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(smooth)
  Loading required package: greybox
  Package "greybox", v0.5.8 loaded.
  This is package "smooth", v2.5.5
  > 
  > test_check("smooth")
  -- 1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40)  --
  suppressWarnings(testModel$xreg) is not null.
  
  == testthat results  ===========================================================
  [ OK: 72 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/snplist.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   2.8Mb
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/4.0gcc8/SongEvo.Rch
eck/vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20populatio
n\%20size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.0gcc8/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
installed size is  5.3Mb
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    R      1.6Mb
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    libs  19.5Mb
installed size is  6.9Mb
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    data   4.7Mb
    libs   2.1Mb
Running examples in 'spatial.tools-Ex.R' failed
The error most likely occurred in:

> ### Name: tahoe_highrez_training
> ### Title: Point and polygon files for use with spatial.tools
> ### Aliases: tahoe_highrez_training
> ### Keywords: data
> 
> ### ** Examples
> 
> library("raster")
Loading required package: sp
> library("rgdal")
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: D:/temp/RtmpWMpdhr/RLIBS_91187b14164e/rgdal/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: D:/temp/RtmpWMpdhr/RLIBS_91187b14164e/rgdal/proj
 Linking to sp version: 1.4-1 
> tahoe_highrez_training_polygons <- readOGR(
+ 	dsn=system.file("external", package="spatial.tools"),layer="tahoe_highrez_training")
OGR data source with driver: ESRI Shapefile 
Source: "D:\temp\RtmpWMpdhr\RLIBS_91187b14164e\spatial.tools\external", layer: "tahoe_highrez_training"
with 8 features
It has 2 fields
> spplot(tahoe_highrez_training_polygons,zcol="Class")
Warning in extend.limits(range(as.numeric(z), finite = TRUE)) :
  NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in seq.default(zrng[1], zrng[2], length.out = cuts + 2) : 
  'from' must be a finite number
Calls: spplot ... <Anonymous> -> levelplot.formula -> seq -> seq.default
Execution halted
installed size is  8.3Mb
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    doc    1.2Mb
    libs   6.8Mb
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spatsoc)
  > 
  > test_check("spatsoc")
  -- 1. Failure: group_times nearest hour with minutes threshold (@test-time.R#271
  ...[] not equal to 3.
  1/1 mismatches
  [1] 4 - 3 == 1
  
  -- 2. Failure: group_times nearest hour with minutes threshold (@test-time.R#287
  ...[] not equal to 3.
  1/1 mismatches
  [1] 4 - 3 == 1
  
  == testthat results  ===========================================================
  [ OK: 241 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: group_times nearest hour with minutes threshold (@test-time.R#271) 
  2. Failure: group_times nearest hour with minutes threshold (@test-time.R#287) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 17.7Mb
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    R      5.3Mb
    doc    4.9Mb
    help   5.3Mb
    libs   1.2Mb
installed size is  5.8Mb
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    libs   5.0Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   3.3Mb
installed size is  6.5Mb
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    data     2.6Mb
    shapes   3.2Mb
installed size is  5.5Mb
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    doc    3.1Mb
    libs   2.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   3.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
    nc    4.5Mb
Running examples in 'stars-Ex.R' failed
The error most likely occurred in:

> ### Name: st_transform
> ### Title: transform features, or warp/resample grids in stars objects to a
> ###   new coordinate reference system
> ### Aliases: st_transform st_transform.stars st_transform_proj.stars
> 
> ### ** Examples
> 
> geomatrix = system.file("tif/geomatrix.tif", package = "stars")
> (x = read_stars(geomatrix))
stars object with 2 dimensions and 1 attribute
attribute(s):
 geomatrix.tif  
 Min.   : 74.0  
 1st Qu.:107.0  
 Median :123.0  
 Mean   :126.8  
 3rd Qu.:132.0  
 Max.   :255.0  
dimension(s):
  from to  offset delta refsys point values    
x    1 20 1841002   1.5     NA  TRUE   NULL [x]
y    1 20 1144003  -1.5     NA  TRUE   NULL [y]
sheared raster with parameters: -5 -5 
> new = st_crs(4326)
> y = st_transform(x, new)
Error in st_transform.stars(x, new) : !is.na(st_crs(x)) is not TRUE
Calls: st_transform -> st_transform.stars -> stopifnot
Execution halted
Error(s) in re-building vignettes:
--- re-building 'stars1.Rmd' using rmarkdown
--- finished re-building 'stars1.Rmd'

--- re-building 'stars2.Rmd' using rmarkdown
--- finished re-building 'stars2.Rmd'

--- re-building 'stars3.Rmd' using rmarkdown
--- finished re-building 'stars3.Rmd'

--- re-building 'stars4.Rmd' using rmarkdown
--- finished re-building 'stars4.Rmd'

--- re-building 'stars5.Rmd' using rmarkdown
Quitting from lines 131-134 (stars5.Rmd) 
Error: processing vignette 'stars5.Rmd' failed with diagnostics:
!is.na(st_crs(x)) is not TRUE
--- failed re-building 'stars5.Rmd'

SUMMARY: processing the following file failed:
  'stars5.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.6Mb
installed size is  5.2Mb
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    data   2.3Mb
    libs   2.5Mb
installed size is  5.5Mb
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    doc    2.6Mb
    libs   2.5Mb
Error(s) in re-building vignettes:
--- re-building 'Details.Rmd' using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Warning: Removed 1 row(s) containing missing values (geom_path).
Quitting from lines 904-907 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
there is no package called 'ggmap'
--- failed re-building 'Details.Rmd'

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

To enable 
caching of data, set `options(tigris_use_cache = TRUE)` in your R script or .Rprofile.

Attaching package: 'tigris'

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

    plot

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

    plot

Loading required package: sp
rgeos version: 0.5-2, (SVN revision 621)
 GEOS runtime version: 3.6.1-CAPI-1.10.1 
 Linking to sp version: 1.4-1 
 Polygon checking: TRUE 

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Loading required package: viridisLite
Warning: Removed 1 row(s) containing missing values (geom_path).
--- finished re-building 'Overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
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    doc    3.0Mb
    libs   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/STRAH.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.4Mb
installed size is  5.6Mb
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    doc    1.6Mb
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installed size is 35.6Mb
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    libs  34.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/STRMPS.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/StroupGLMM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SubVis.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/superbiclust.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.2Mb
    libs   2.2Mb
installed size is 15.6Mb
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    libs  14.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
Running examples in 'SympluR-Ex.R' failed
The error most likely occurred in:

> ### Name: symplurContentRetweets
> ### Title: Symplur API - Content/Retweets
> ### Aliases: symplurContentRetweets
> ### Keywords: content retweets
> 
> ### ** Examples
> 
> LCSMDemoDataContentRetweets <- symplurContentRetweets(
+     "09/01/2017",
+     "09/08/2017",
+     databases = "#LCSMDemoData",
+     50)
What is your Symplur API clientId? If none, just hit enter to try #LCSMDemoData: 
What is your Symplur API clientSecret? If none, just hit enter to try #LCSMDemoData: 
Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE,  : 
  arguments imply differing number of rows: 0, 1
Calls: symplurContentRetweets ... as.data.frame -> as.data.frame.list -> do.call -> <Anonymous>
Execution halted
Documented arguments not in \usage in documentation object 'bytable':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/TcGSA.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.9Mb
    libs   2.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Running examples in 'TeachingDemos-Ex.R' failed
The error most likely occurred in:

> ### Name: simfun
> ### Title: Create a function to simulate data
> ### Aliases: simfun
> ### Keywords: datagen design
> 
> ### ** Examples
> 
> # Create a function to simulate heights for a given dataset
> 
> simheight <- simfun( {h <- c(64,69); height<-h[sex]+ rnorm(10,0,3)}, drop='h' )
> 
> my.df <- data.frame(sex=rep(c('Male','Female'),each=5))
> simdat <- simheight(my.df)
> t.test(height~sex, data=simdat)
Error in t.test.formula(height ~ sex, data = simdat) : 
  grouping factor must have exactly 2 levels
Calls: t.test -> t.test.formula
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   3.2Mb
installed size is 83.8Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    gdal   3.8Mb
    libs  72.5Mb
    proj   5.0Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs      13.9Mb
    tessdata  14.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.2Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    2.9Mb
    libs   2.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.9Mb
    libs      2.1Mb
Running examples in 'tidyHeatmap-Ex.R' failed
The error most likely occurred in:

> ### Name: heatmap
> ### Title: Creates a 'ComplexHeatmap' plot from 'tbl'
> ### Aliases: heatmap
> 
> ### ** Examples
> 
> 
> library(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

> tidyHeatmap::N52 %>%
+ group_by( `Cell type`) %>%
+ tidyHeatmap::heatmap(
+  .horizontal = UBR,
+  .vertical = symbol_ct,
+  .abundance = `read count normalised log`,
+  annotation = CAPRA_TOTAL
+ )
Adding missing grouping variables: `Cell type`
Error: x should be in mm unit
Execution halted
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using knitr
Quitting from lines 55-63 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
x should be in mm unit
--- failed re-building 'introduction.Rmd'

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

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

> ### Name: readTIFF
> ### Title: Read a bitmap image stored in the TIFF format
> ### Aliases: readTIFF
> ### Keywords: IO
> 
> ### ** Examples
> 
> # read a sample file (R logo)
> img <- readTIFF(system.file("img", "Rlogo.tiff", package="tiff"))
Found the following significant warnings:
  Warning: replacing previous import 'sf::st_make_valid' by 'lwgeom::st_make_valid' when loading 'tmap'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/tmap.Rcheck/00install.out' for details.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    examples  19.5Mb
    include    2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Tnseq.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/topologyGSA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/trackr.Rcheck/00install.out' for details.
Running examples in 'traitdataform-Ex.R' failed
The error most likely occurred in:

> ### Name: rbind.traitdata
> ### Title: Combine trait datasets
> ### Aliases: rbind.traitdata
> 
> ### ** Examples
> 
> 
> pulldata("carabids")
The dataset 'carabids' is now available for use! 

> 
> dataset1 <- as.traitdata(carabids,
+   taxa = "name_correct",
+   traits = c("body_length", "antenna_length", "metafemur_length"),
+   units = "mm",
+   keep = c(datasetID = "source_measurement", measurementRemarks = "note"),
+   metadata = as.metadata(
+     bibliographicCitation = c(
+         "van der Plas et al. (2017) Methods in Ecol. & Evol., doi: 10.1111/2041-210x.12728"
+        ),
+     author = "Fons van der Plas",
+     license = "http://creativecommons.org/publicdomain/zero/1.0/"
+     )
+ )
Input is taken to be a species -- trait matrix. If this is not the case, please provide parameters!
> 
> 
> traits1 <- as.thesaurus(
+  body_length = as.trait("body_length",
+    expectedUnit = "mm", valueType = "numeric",
+    identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Body_length"),
+  antenna_length = as.trait("antenna_length",
+    expectedUnit = "mm", valueType = "numeric",
+    identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Antenna_length"),
+  metafemur_length = as.trait("metafemur_length",
+    expectedUnit = "mm", valueType = "numeric",
+    identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length")
+ )
> 
> dataset1Std <- standardize.traits(dataset1, thesaurus = traits1)
Error in UseMethod("droplevels") : 
  no applicable method for 'droplevels' applied to an object of class "character"
Calls: standardize.traits -> droplevels
Execution halted
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(traitdataform)
  > 
  > test_check("traitdataform")
  -- 1. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10)  ---------
  Value hashes to 2448e3596a, not bc9f97d273
  
  -- 2. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#11)  ---------
  Value hashes to 4381d5bd4d, not 74f9a02a12
  
  -- 3. Error: mapping of traits based on thesaurus works (@test.standardize.R#64)
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. traitdataform::standardize_traits(dataset2, thesaurus = traits2)
   2. base::droplevels(subset(out, traitNameStd == i)$traitUnitStd)
  
  -- 4. Error: factor level harmonizationworks (@test.standardize.R#81)  ---------
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. traitdataform::standardize_traits(dd1)
   2. base::droplevels(subset(out, traitNameStd == i)$traitUnit)
  
  == testthat results  ===========================================================
  [ OK: 55 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10) 
  2. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#11) 
  3. Error: mapping of traits based on thesaurus works (@test.standardize.R#64) 
  4. Error: factor level harmonizationworks (@test.standardize.R#81) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'traitdataform.Rmd' using rmarkdown
Quitting from lines 310-312 (traitdataform.Rmd) 
Error: processing vignette 'traitdataform.Rmd' failed with diagnostics:
no applicable method for 'droplevels' applied to an object of class "character"
--- failed re-building 'traitdataform.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/treeDA.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   2.0Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  11.4Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tricolore)
  > 
  > test_check('tricolore')
  -- 1. Error: NA, Inf, NaNs in input return NA in output (@test-global.R#82)  ---
  "plot.title.position" is not a valid theme element name.
  Backtrace:
   1. tricolore::Tricolore(P, "a", "b", "c", breaks = Inf)
   2. tricolore:::ColorKeyTricolore(...)
   3. tricolore:::BasicKey(...)
   4. ggtern:::`+.gg`(...)
   5. ggtern:::add_ggplot(e1, e2, e2name)
   6. ggtern:::update_theme(p$theme, object)
   9. base::mapply(validate_element, elements, names(elements))
  
  == testthat results  ===========================================================
  [ OK: 33 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: NA, Inf, NaNs in input return NA in output (@test-global.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'choropleth_maps_with_tricolore.Rmd' using rmarkdown
Quitting from lines 48-50 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
"plot.title.position" is not a valid theme element name.
--- failed re-building 'choropleth_maps_with_tricolore.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ttScreening.Rcheck/00install.out' for details.
txtacf: no visible binding for global variable 'na.fail'
txtacf: no visible global function definition for 'acf'
txtboxplot : <anonymous>: no visible global function definition for
  'boxplot.stats'
txtboxplot: no visible global function definition for 'boxplot.stats'
txtdensity: no visible global function definition for 'density'
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs        4.7Mb
installed size is 83.0Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.3Mb
    gdal      3.8Mb
    libs     69.6Mb
    proj      5.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs   2.9Mb
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  23.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/VALERIE.Rcheck/00install.out' for details.
installed size is 79.8Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      3.8Mb
    libs     69.5Mb
    proj      5.0Mb
Found the following significant warnings:
  Warning: No CA bundle found. SSL validation disabled.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/VarfromPDB.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/vhcub.Rcheck/00install.out' for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/viromeBrowser.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/VSE.Rcheck/00install.out' for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Error(s) in re-building vignettes:
--- re-building 'wCorrArguments.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rchec
k/vign_test/wCorr/vignettes/wCorrArguments_files/figure-latex/ML\%20RMSE\%20plo
t-1.pdf' not found.

Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrArguments.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrArguments.log for more info.
--- failed re-building 'wCorrArguments.Rmd'

--- re-building 'wCorrFormulas.Rmd' using rmarkdown
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rchec
k/vign_test/wCorr/vignettes/wCorrFormulas_files/figure-latex/bias\%20Versus\%20
rho-1.pdf' not found.

Error: processing vignette 'wCorrFormulas.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrFormulas.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrFormulas.log for more info.
--- failed re-building 'wCorrFormulas.Rmd'

SUMMARY: processing the following files failed:
  'wCorrArguments.Rmd' 'wCorrFormulas.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/WGCNA.Rcheck/00install.out' for details.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wilson)
  
  Attaching package: 'wilson'
  
  The following object is masked from 'package:stats':
  
      heatmap
  
  > 
  > test_check("wilson")
  -- 1. Error: complexHeatmap is downloadable (@test-download.R#31)  -------------
  old version of unit class is no longer allowed
  Backtrace:
   1. ComplexHeatmap::Heatmap(mtcars)
   2. grid:::Ops.unit(row_dend_width, ht_opt$DENDROGRAM_PADDING)
   3. grid:::as.unit(e2)
  
  Error in as.unit(e2) : old version of unit class is no longer allowed
  [1] "Error in as.unit(e2) : old version of unit class is no longer allowed\n"
  attr(,"class")
  [1] "try-error"
  attr(,"condition")
  <simpleError in as.unit(e2): old version of unit class is no longer allowed>
  == testthat results  ===========================================================
  [ OK: 54 | SKIPPED: 5 | WARNINGS: 22 | FAILED: 1 ]
  1. Error: complexHeatmap is downloadable (@test-download.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/x13binary.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  RSDTD.c:298:23: warning: passing argument 2 of 'xmlHashScan' from incompatible pointer type [-Wincompatible-pointer-types]
  RSDTD.c:372:23: warning: passing argument 2 of 'xmlHashScan' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/XML.Rcheck/00install.out' for details.
Running examples in 'Xplortext-Ex.R' failed
The error most likely occurred in:

> ### Name: LexHCca
> ### Title: Hierarchical Clustering of Documents on Textual Correspondence
> ###   Analysis Coordinates (LexHCca)
> ### Aliases: LexHCca
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(open.question)
> res.TD<-TextData(open.question, var.text=c(9,10), Fmin=10, Dmin=10, stop.word.tm=TRUE,
+         context.quali=c("Gender","Age_Group","Education"), context.quanti=c("Age"))
> res.LexCA<-LexCA(res.TD, graph=FALSE, ncp=8)
Error in which(unlist(lapply(listModa, is.numeric))) : 
  argument to 'which' is not logical
Calls: LexCA -> as.matrix -> t -> tab.disjonctif -> which
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      2.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   2.4Mb
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(aoos)
  > 
  > test_check("aoos")
  ── 1. Failure: Type inheritance (@test-S4-types.R#75)  ─────────────────────────
  inherits(Child(), "Test2") isn't true.
  
  ── 2. Failure: Type with VIRTUAL (@test-S4-types.R#111)  ───────────────────────
  names(Test(x = 2)) == "x" isn't true.
  
  ── 3. Failure: Type with VIRTUAL (@test-S4-types.R#112)  ───────────────────────
  inherits(Test(), "Type") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 187 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Type inheritance (@test-S4-types.R#75) 
  2. Failure: Type with VIRTUAL (@test-S4-types.R#111) 
  3. Failure: Type with VIRTUAL (@test-S4-types.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(apa)
  > 
  > test_check("apa")
  ── 1. Error: Output for anova_apa: repeated-measures ANOVA (@test-anova-apa.R#13
  Assigned data `<list>` must be compatible with existing data.
  ℹ Error occurred for column `df_n`.
  ✖ No common type for `value` <character> and `x` <double>.
  Backtrace:
    1. apa::anova_apa(...)
    2. apa:::anova_apa_afex(x, effect, sph_corr, es, format, info, print)
    7. tibble:::`[<-.tbl_df`(...)
    8. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   10. base::tryCatch(...)
   11. base:::tryCatchList(expr, classes, parentenv, handlers)
   12. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. value[[3L]](cond)
  
  ── 2. Error: Output for anova_apa: factorial repeated-measures ANOVA (@test-anov
  Assigned data `<list>` must be compatible with existing data.
  ℹ Error occurred for column `df_n`.
  ✖ No common type for `value` <character> and `x` <double>.
  Backtrace:
    1. apa::anova_apa(...)
    2. apa:::anova_apa_afex(x, effect, sph_corr, es, format, info, print)
    7. tibble:::`[<-.tbl_df`(...)
    8. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   10. base::tryCatch(...)
   11. base:::tryCatchList(expr, classes, parentenv, handlers)
   12. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 105 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 2 ]
  1. Error: Output for anova_apa: repeated-measures ANOVA (@test-anova-apa.R#135) 
  2. Error: Output for anova_apa: factorial repeated-measures ANOVA (@test-anova-apa.R#181) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [10s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcmaps)
  Loading required package: sf
  Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 7.0.0
  > 
  > test_check("bcmaps")
  ── 1. Error: works with self-intersections: sf (@test-fix_geo_problems.R#94)  ──
  'st_make_valid' is not an exported object from 'namespace:lwgeom'
  Backtrace:
   1. testthat::expect_message(...)
   7. bcmaps:::fix_geo_problems.sf(st_as_sf(p4))
   8. lwgeom::st_make_valid
   9. base::getExportedValue(pkg, name)
  
  ── 2. Error: works with other problems: sf (@test-fix_geo_problems.R#106)  ─────
  'st_make_valid' is not an exported object from 'namespace:lwgeom'
  Backtrace:
   1. testthat::expect_message(...)
   7. bcmaps:::fix_geo_problems.sf(st_as_sf(p7))
   8. lwgeom::st_make_valid
   9. base::getExportedValue(pkg, name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 57 | SKIPPED: 12 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: works with self-intersections: sf (@test-fix_geo_problems.R#94) 
  2. Error: works with other problems: sf (@test-fix_geo_problems.R#106) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Biograph.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(biscale)
  > 
  > test_check("biscale")
  ── 1. Error: sf warning is triggered (@test_bi_class.R#10)  ────────────────────
  All columns in a tibble must be vectors.
  ✖ Column `geometry` is a `sfc_POLYGON/sfc` object.
  Backtrace:
    1. testthat::expect_warning(...)
    6. biscale::bi_class(...)
    8. dplyr:::mutate.data.frame(...)
   11. dplyr::tbl_df(.data)
   13. tibble:::as_tibble.data.frame(data, .name_repair = "check_unique")
   14. tibble:::lst_to_tibble(unclass(x), .rows, .name_repair)
   15. tibble:::check_valid_cols(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 82 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: sf warning is triggered (@test_bi_class.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘broom_mixed_intro.rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Registered S3 methods overwritten by 'broom.mixed':
  method         from 
  augment.lme    broom
  augment.merMod broom
  glance.lme     broom
  glance.merMod  broom
  glance.stanreg broom
  tidy.brmsfit   broom
  tidy.gamlss    broom
  tidy.lme       broom
  tidy.merMod    broom
  tidy.rjags     broom
  tidy.stanfit   broom
  tidy.stanreg   broom
Loading required package: brms
Loading required package: Rcpp
Loading 'brms' package (version 2.12.0). Useful instructions
can be found by typing help('brms'). A more detailed introduction
to the package is available through vignette('brms_overview').

Attaching package: 'brms'

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

    ar

Loading required package: dotwhisker
Loading required package: ggplot2
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 68-82 (broom_mixed_intro.rmd) 
Error: processing vignette 'broom_mixed_intro.rmd' failed with diagnostics:
Aesthetics must be either length 1 or the same as the data (6): xmin and xmax
--- failed re-building ‘broom_mixed_intro.rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:1: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/cairoDevice.Rcheck/00install.out’ for details.
Running examples in ‘cartography-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: smoothLayer
> ### Title: Smooth Layer
> ### Aliases: smoothLayer
> 
> ### ** Examples
> 
> library(sf)
Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 7.0.0
> mtq <- st_read(system.file("gpkg/mtq.gpkg", package="cartography"))
Reading layer `mtq' from data source `/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cartography/gpkg/mtq.gpkg' using driver `GPKG'
Simple feature collection with 34 features and 7 fields
geometry type:  MULTIPOLYGON
dimension:      XY
bbox:           xmin: 690574 ymin: 1592536 xmax: 735940.2 ymax: 1645660
projected CRS:  WGS 84 / UTM zone 20N
> smoothLayer(x = mtq, var = 'POP',
+             span = 4000, beta = 2,
+             mask = mtq, border = NA,
+             col = carto.pal(pal1 = 'wine.pal', n1 = 8),
+             legend.title.txt = "Population\nPotential",
+             legend.pos = "topright", legend.values.rnd = 0)
Error: 'SpatialPosition' package needed for this function to work. Please install it.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CensMFM.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [202s/216s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clubSandwich)
  Registered S3 method overwritten by 'clubSandwich':
    method    from    
    bread.mlm sandwich
  > 
  > test_check("clubSandwich")
  ── 1. Failure: Order doesn't matter. (@test_lmerMod.R#153)  ────────────────────
  `Wald_fit` not equal to `Wald_scramble`.
  Component 19: Component 4: Mean relative difference: 1.550445e-08
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 754 | SKIPPED: 11 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Order doesn't matter. (@test_lmerMod.R#153) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [10s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 612 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ctsem.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./src/common/Random.c:105:5: warning: ‘memcpy’ pointer overflow between offset 0 and size [-4, 9223372036854775807] [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/cubature.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: ignoring environment value of R_HOME
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/datasailr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'glmer(y ~ items + (1 | ': unused argument (REML = FALSE) 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/difR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/edbuildmapr.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [17s/19s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Failure: moves_calc gets the correct results (@test-calculators.R#210)  ──
  `moves` not equal to `correct_result`.
  Component "sid": Modes: character, numeric
  Component "sid": Attributes: < target is NULL, current is list >
  Component "sid": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 509 | SKIPPED: 0 | WARNINGS: 29 | FAILED: 1 ]
  1. Failure: moves_calc gets the correct results (@test-calculators.R#210) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(epikit)
  > 
  > test_check("epikit")
  ── 1. Failure: case_fatality_rate_df will add a total row to stratified analysis
  `iris_res` not equal to `iris_n`.
  Incompatible type for column `Species`: x character, y factor
  
  ── 2. Failure: case_fatality_rate_df will add a total row to stratified analysis
  `iris_res` not equal to `iris_n`.
  Incompatible type for column `Species`: x character, y factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 107 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: case_fatality_rate_df will add a total row to stratified analysis (@test-proportion.R#152) 
  2. Failure: case_fatality_rate_df will add a total row to stratified analysis and merge CI (@test-proportion.R#173) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(etl)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("etl")
  ── 1. Failure: create ETL works (@test-etl.R#114)  ─────────────────────────────
  `create_etl_package\(path, open = FALSE\)` does not match "active project".
  Actual value: "Package: scorecard\\nTitle: What the Package Does \(One Line, Title Case\)\\nVersion: 0\.0\.0\.9000\\nAuthors@R \(parsed\):\\n    \* First Last <first\.last@example\.com> \[aut, cre\] \(YOUR-ORCID-ID\)\\nDescription: What the package does \(one paragraph\)\.\\nLicense: `use_mit_license\(\)`, `use_gpl3_license\(\)` or friends to pick a\\n    license\\nEncoding: UTF-8\\nLazyData: true\\nRoxygen: list\(markdown = TRUE\)\\nRoxygenNote: 7\.1\.0"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 27 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: create ETL works (@test-etl.R#114) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [26s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fable)
  Loading required package: fabletools
  > 
  > test_check("fable")
  ── 1. Failure: Automatic ETS selection (@test-ets.R#14)  ───────────────────────
  tidy(model(UKLungDeaths[1:24, ], ETS(mdeaths)))$estimate not equal to c(1, 2134).
  names for target but not for current
  
  ── 2. Failure: Manual ETS selection (@test-ets.R#51)  ──────────────────────────
  tidy(refit(fable_fit, USAccDeaths_tbl))$estimate == tidy(fable_fit)$estimate not identical to c(rep(TRUE, 2), rep(FALSE, 12)).
  names for target but not for current
  
  ── 3. Failure: Manual ETS selection (@test-ets.R#62)  ──────────────────────────
  tidy(fable_fit)$estimate[3:14] not identical to c(cmp$level[12], cmp$season[12:2]).
  names for target but not for current
  
  ── 4. Failure: Manual ETS selection (@test-ets.R#87)  ──────────────────────────
  coef$estimate[1:4] not identical to c(0.5, 0.006, 1e-04, 0.975).
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 100 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Automatic ETS selection (@test-ets.R#14) 
  2. Failure: Manual ETS selection (@test-ets.R#51) 
  3. Failure: Manual ETS selection (@test-ets.R#62) 
  4. Failure: Manual ETS selection (@test-ets.R#87) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Killed
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fredr)
  > 
  > test_check("fredr")
  ── 1. Failure: fredr_docs throws errors on invalid endpoints (@test_docs.R#8)  ─
  `fredr_docs(endpoint = "foo")` did not throw an error.
  
  ── 2. Failure: fredr_docs throws errors on invalid endpoints (@test_docs.R#9)  ─
  `fredr_docs(endpoint = "foo", params = TRUE)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 65 | SKIPPED: 38 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: fredr_docs throws errors on invalid endpoints (@test_docs.R#8) 
  2. Failure: fredr_docs throws errors on invalid endpoints (@test_docs.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.R’ [28s/31s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > suppressWarnings(RNGversion("3.5.0"))
  > 
  > test_check('ggfortify')
  Loading required package: ggfortify
  Loading required package: ggplot2
  ── 1. Failure: fortify.survfit works for simple data (@test-surv.R#107)  ───────
  `fortified` not equal to `expected`.
  Component "std.err": Mean relative difference: 1.398096
  Component "upper": Mean relative difference: 0.4055626
  Component "lower": Mean relative difference: 0.6532618
  
  ── 2. Failure: fortify.survfit works for simple data (@test-surv.R#118)  ───────
  `fortified` not equal to `expected`.
  Component "std.err": Mean relative difference: 1.398096
  Component "upper": Mean relative difference: 0.4055626
  Component "lower": Mean relative difference: 0.6532618
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 735 | SKIPPED: 47 | WARNINGS: 2 | FAILED: 2 ]
  1. Failure: fortify.survfit works for simple data (@test-surv.R#107) 
  2. Failure: fortify.survfit works for simple data (@test-surv.R#118) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gglogo-alphabet.Rmd’ using rmarkdown

Attaching package: 'gglogo'

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

    fortify

Killed
Found the following significant warnings:
  Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial") 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GWAF.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [16s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hereR)
  > 
  > test_check("hereR")
  ── 1. Error: isoline works  ────────────────────────────────────────────────────
  'st_make_valid' is not an exported object from 'namespace:lwgeom'
  Backtrace:
   1. hereR::isoline(poi = poi, aggregate = TRUE)
   2. lwgeom::st_make_valid
   3. base::getExportedValue(pkg, name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 110 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: isoline works 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘acf.Rmd’ using rmarkdown
--- finished re-building ‘acf.Rmd’

--- re-building ‘inspect.Rmd’ using rmarkdown
Quitting from lines 101-106 (inspect.Rmd) 
Error: processing vignette 'inspect.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘inspect.Rmd’

--- re-building ‘test.Rmd’ using rmarkdown
Quitting from lines 187-200 (test.Rmd) 
Error: processing vignette 'test.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘test.Rmd’

SUMMARY: processing the following files failed:
  ‘inspect.Rmd’ ‘test.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/JavaGD.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [205s/225s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jpndistrict)
  This package provide map data is based on the Digital Map 25000 (Map
  Image) published by Geospatial Information Authority of Japan (Approval
  No.603FY2017 information usage <http://www.gsi.go.jp>)
  > 
  > test_check("jpndistrict")
  trying URL 'http://nlftp.mlit.go.jp/ksj/gml/data/P34/P34-14/P34-14_47_GML.zip'
  Content type 'application/zip' length 9427 bytes
  ==================================================
  downloaded 9427 bytes
  
  options:        ENCODING=cp932 
  Reading layer `P34-14_47' from data source `/tmp/RtmpGUhWOZ/P34-14_47_GML/P34-14_47.shp' using driver `ESRI Shapefile'
  Simple feature collection with 65 features and 4 fields
  geometry type:  POINT
  dimension:      XY
  bbox:           xmin: 123.0045 ymin: 24.06092 xmax: 131.2989 ymax: 27.03917
  geographic CRS: JGD2000
  ── 1. Error: Data (@test-util.R#4)  ────────────────────────────────────────────
  'st_make_valid' is not an exported object from 'namespace:lwgeom'
  Backtrace:
    1. testthat::expect_length(export_pref_80km_mesh(1), 40L)
    4. jpndistrict:::export_pref_80km_mesh(1)
    3. jpndistrict::jpn_pref(pref_code = code)
   11. lwgeom::st_make_valid(.)
   14. base::getExportedValue(pkg, name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 91 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Data (@test-util.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [63s/69s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jtools)
  > 
  > 
  > test_check("jtools")
  ── 1. Error: plot_coefs works with brms (@test-export-summs.R#294)  ────────────
  Aesthetics must be either length 1 or the same as the data (8): xmin and xmax
  Backtrace:
    1. testthat::expect_silent(print(plot_coefs(bfit1) + ggtitle("basic brms fit")))
   10. ggplot2:::print.ggplot(plot_coefs(bfit1) + ggtitle("basic brms fit"))
   12. ggplot2:::ggplot_build.ggplot(x)
   13. ggplot2:::by_layer(function(l, d) l$compute_aesthetics(d, plot))
   14. ggplot2:::f(l = layers[[i]], d = data[[i]])
   15. l$compute_aesthetics(d, plot)
   16. ggplot2:::f(..., self = self)
   17. ggplot2:::check_aesthetics(evaled, n)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 357 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 1 ]
  1. Error: plot_coefs works with brms (@test-export-summs.R#294) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘konfound-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mkonfound
> ### Title: Perform meta-analyses including sensitivity analysis
> ### Aliases: mkonfound
> 
> ### ** Examples
> 
> d <- read.csv("https://msu.edu/~kenfrank/example%20dataset%20for%20mkonfound.csv")
Warning in file(file, "rt") :
  URL 'https://msu.edu/~kenfrank/example%20dataset%20for%20mkonfound.csv': status was 'Failure when receiving data from the peer'
Error in file(file, "rt") : 
  cannot open the connection to 'https://msu.edu/~kenfrank/example%20dataset%20for%20mkonfound.csv'
Calls: read.csv -> read.table -> file
Execution halted
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: 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]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: 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]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: 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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MLTA_Gollini_2019.Rmd’ using rmarkdown
Loading required package: MASS
Loading required package: ergm
Loading required package: network
network: Classes for Relational Data
Version 1.16.0 created on 2019-11-30.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


ergm: version 3.10.4, created on 2019-06-10
Copyright (c) 2019, Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Carter T. Butts, University of California -- Irvine
                    Steven M. Goodreau, University of Washington
                    Pavel N. Krivitsky, University of Wollongong
                    Martina Morris, University of Washington
                    with contributions from
                    Li Wang
                    Kirk Li, University of Washington
                    Skye Bender-deMoll, University of Washington
                    Chad Klumb
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ergm").

NOTE: Versions before 3.6.1 had a bug in the implementation of the bd()
constriant which distorted the sampled distribution somewhat. In
addition, Sampson's Monks datasets had mislabeled vertices. See the
NEWS and the documentation for more details.

NOTE: Some common term arguments pertaining to vertex attribute and
level selection have changed in 3.10.0. See terms help for more
details. Use 'options(ergm.term=list(version="3.9.4"))' to use old
behavior.

Killed
Running ‘testthat.R’ [10m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(matrixTests)
  > 
  > test_check("matrixTests")
  Killed
Running ‘testthat.R’ [148s/164s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  ── 1. Failure: Summing counts per taxon (@test--calculations.R#103)  ───────────
  sum(x$data$tax_data$`700035949`) not equal to result$`700035949`[1].
  names for current but not for target
  
  ── 2. Failure: Summing counts per taxon (@test--calculations.R#126)  ───────────
  `total_counts` not equal to result$total[1].
  names for current but not for target
  
  ── 3. Failure: Parsing the UNITE general release fasta (@test--parsers_and_write
  result$data$tax_data$unite_seq[5] not equal to "CCAAATCATGTCTCCCGGCCGCAAGGCAGGTGCAGGCGTTTAACCCTTTGTGAACCAAAAAACCTTTCGCTTCGGCAGCAGCTCGGTTGGAGACAGCCTCTGTGTCAGCCTGCCGCTAGCACCAATTATCAAAACTTGCGGTTAGCAACATTGTCTGATTACCAAATTTTCGAATGAAAATCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAACGCGATAGTTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCATTGGTATTCCATTGGGCATGTCTGTTTGAGCGTCATTACAACCCTCGGTCACCACCGGTTTTGAGCGAGCAGGGTCTTCGGATCCAGCTGGCTTTAAAGTTGTAAGCTCTGCTGGCTGCTCGGCCCAACCAGAACATAGTAAAATCATGCTTGTTCAAGGTTCGCGGTCGAAGCGGTACGGCCTGAACAATACCTACCACCTCTTAGG".
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 93 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Summing counts per taxon (@test--calculations.R#103) 
  2. Failure: Summing counts per taxon (@test--calculations.R#126) 
  3. Failure: Parsing the UNITE general release fasta (@test--parsers_and_writers.R#119) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
Killed
Error(s) in re-building vignettes:
  ...
--- re-building ‘milr-intro.Rmd’ using rmarkdown
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.8390.
trying URL ‘http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz’
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.2909.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Killed
Running examples in ‘MIMSunit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: import_mhealth_csv
> ### Title: Import raw multi-channel accelerometer data stored in mHealth
> ###   Specification
> ### Aliases: import_mhealth_csv
> 
> ### ** Examples
> 
>   default_ops = options()
>   options(digits.secs=3)
>   # Use the sample mhealth csv file provided by the package
>   filepath = system.file('extdata', 'mhealth.csv', package='MIMSunit')
>   filepath
[1] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/MIMSunit/extdata/mhealth.csv"
> 
>   # Load the file
>   df = import_mhealth_csv(filepath)
Error: Assigned data `as.character(df[, factor_cols])` must be compatible with existing data.
✖ Existing data has 5000 rows.
✖ Assigned data has 0 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─MIMSunit::import_mhealth_csv(filepath)
 2.   ├─base::`[<-`(`*tmp*`, , factor_cols, value = character(0))
 3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, , factor_cols, value = character(0))
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
Running ‘testthat.R’ [34s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OpenLand)
  > 
  > test_check("OpenLand")
  ── 1. Error: Behavior of summary_map (@test_generalfunctions.R#53)  ────────────
  Assigned data `c(as.numeric(names(value_map)[i]), value_map[[i]])` must be compatible with row subscript `i`.
  ✖ 1 row must be assigned.
  ✖ Assigned data has 2 rows.
  ℹ Only vectors of size 1 are recycled.
  Backtrace:
    1. testthat::expect_silent(...)
    9. OpenLand::summary_map(...)
   11. tibble:::`[<-.tbl_df`(`*tmp*`, i, c(1:2), value = c(1, 1983))
   12. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   13. tibble:::vectbl_recycle_rhs(...)
   14. base::tryCatch(...)
   15. base:::tryCatchList(expr, classes, parentenv, handlers)
   16. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   17. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 112 | SKIPPED: 0 | WARNINGS: 24 | FAILED: 1 ]
  1. Error: Behavior of summary_map (@test_generalfunctions.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘pancor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getExprSet
> ### Title: download exprSet data
> ### Aliases: getExprSet
> 
> ### ** Examples
> 
> temp_dir <- tempdir()
> getExprSet(file = "test.txt", outdir = temp_dir)
trying URL 'ftp://119.29.67.25/pub/test.txt'
Content type 'unknown' length 5 bytes

Warning in download.file(file_url, file.path(outdir, file)) :
  downloaded length 0 != reported length 5
Warning in download.file(file_url, file.path(outdir, file)) :
  cannot open URL 'ftp://119.29.67.25/pub/test.txt': FTP status was '425 Cannot open data connection'
Error in download.file(file_url, file.path(outdir, file)) : 
  cannot open URL 'ftp://119.29.67.25/pub/test.txt'
Calls: getExprSet -> download.file
Execution halted
Found the following significant warnings:
  Warning: `data_frame()` is deprecated as of tibble 1.1.0.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/poio.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [191s/229s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(portalr)
  > 
  > test_check("portalr")
  ── 1. Failure: default data path functions work if unset (@test-01-data-retrieva
  `m` does not match "Call `usethis::edit_r_environ\\(\\)` to open '.Renviron'".
  Actual value: ""
  
  ── 2. Failure: default data path functions work if unset (@test-01-data-retrieva
  `m` does not match "Store your data path with a line like:".
  Actual value: ""
  
  ── 3. Failure: default data path functions work if unset (@test-01-data-retrieva
  `m` does not match "PORTALR_DATA_PATH=".
  Actual value: ""
  
  ── 4. Failure: default data path functions work if unset (@test-01-data-retrieva
  `m` does not match "Make sure '.Renviron' ends with a newline!".
  Actual value: ""
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 194 | SKIPPED: 10 | WARNINGS: 4 | FAILED: 4 ]
  1. Failure: default data path functions work if unset (@test-01-data-retrieval.R#107) 
  2. Failure: default data path functions work if unset (@test-01-data-retrieval.R#108) 
  3. Failure: default data path functions work if unset (@test-01-data-retrieval.R#109) 
  4. Failure: default data path functions work if unset (@test-01-data-retrieval.R#110) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘run-all.R’ [10s/20s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("ProjectTemplate")
  Loading required package: ProjectTemplate
  ── 1. Failure: Custom configuration is added to config (@test-add_config.R#12)  
  `load.project()` generated warnings:
  * 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
  
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | Example tests
  ✔ |   1       | Example tests
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | Example tests
  ✔ |   1       | Example tests
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] TRUE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 852 | SKIPPED: 4 | WARNINGS: 281 | FAILED: 1 ]
  1. Failure: Custom configuration is added to config (@test-add_config.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/qtbase.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [6s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ralger)
  > 
  > test_check("ralger")
  ── 1. Failure: scrap() function (@test-scrap.R#4)  ─────────────────────────────
  scrap(link = "https://www.imdb.com/chart/top/", node = ".titleColumn a") not equal to unlist(...).
  6/250 mismatches
  x[173]: "Fargo"
  y[173]: "Stalker"
  
  x[174]: "Stalker"
  y[174]: "Fargo"
  
  x[204]: "Stand by Me - Das Geheimnis eines Sommers"
  y[204]: "Network"
  
  x[205]: "Network"
  y[205]: "Stand by Me - Das Geheimnis eines Sommers"
  
  x[241]: "Lagaan: Once Upon a Time in India"
  y[241]: "The Terminator"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: scrap() function (@test-scrap.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘rasciidoc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rasciidoc
> ### Title: Render an 'asciidoc' File
> ### Aliases: rasciidoc
> 
> ### ** Examples
> 
> wd <- file.path(tempdir(), "rasciidoc")
> dir.create(wd)
> file  <- system.file("files", "minimal", "knit.asciidoc",
+                      package = "rasciidoc")
> file.copy(file, wd)
[1] TRUE
> rasciidoc::rasciidoc(file.path(wd, basename(file)), "-b docbook")
Due to the CRAN policy of not writing "anywhere else on the file system apart from the R session's temporary directory" we work on a temporary copy of /tmp/RtmpX1kgAo/rasciidoc/knit.asciidoc.
Thus all internal sourcing and internal links will be broken and any output is written to /tmp/RtmpX1kgAo. Set the option "write_to_disk" to TRUE (using
	options("write_to_disk" = TRUE)
) to bypass this. You may want to include the above line into your ~/.Rprofile.
Warning in rasciidoc::rasciidoc(file.path(wd, basename(file)), "-b docbook") :
  Can't find program `source-highlight`. Please install first (http://www.gnu.org/software/src-highlite/).
Warning in rasciidoc::rasciidoc(file.path(wd, basename(file)), "-b docbook") :
  Can't find program `asciidoc`. Please install first (www.asciidoc.org).
Error: invalid version specification ‘2.7.18rc1’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘An_Introduction_to_rasciidoc.Rasciidoc’ using rasciidoc
Warning in run_knit(file_name, knit = knit, envir = envir, write_to_disk = write_to_disk) :
  Setting option knit to TRUE based on the file contents!


processing file: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rasciidoc.Rcheck/vign_test/rasciidoc/vignettes/An_Introduction_to_rasciidoc.Rasciidoc
  ordinary text without R code

label: unnamed-chunk-1
  ordinary text without R code

label: unnamed-chunk-2
  ordinary text without R code

label: unnamed-chunk-3
  ordinary text without R code

label: unnamed-chunk-4
  ordinary text without R code

label: unnamed-chunk-5
  ordinary text without R code

label: unnamed-chunk-6
  ordinary text without R code

label: unnamed-chunk-7
  ordinary text without R code

output file: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rasciidoc.Rcheck/vign_test/rasciidoc/vignettes/An_Introduction_to_rasciidoc.asciidoc

Warning in rasciidoc(file_name = adoc, write_to_disk = write_to_disk, asciidoc_args) :
  Can't find program `source-highlight`. Please install first (http://www.gnu.org/software/src-highlite/).
Warning in rasciidoc(file_name = adoc, write_to_disk = write_to_disk, asciidoc_args) :
  Can't find program `asciidoc`. Please install first (www.asciidoc.org).
Error: processing vignette 'An_Introduction_to_rasciidoc.Rasciidoc' failed with diagnostics:
invalid version specification ‘2.7.18rc1’
--- failed re-building ‘An_Introduction_to_rasciidoc.Rasciidoc’

SUMMARY: processing the following file failed:
  ‘An_Introduction_to_rasciidoc.Rasciidoc’

Error: Vignette re-building failed.
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’ using rmarkdown
Loading required package: rJava
Loading required package: Rdroolsjars

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: 'purrr'

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.thoughtworks.xstream.core.util.Fields (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rdroolsjars/java/xstream-1.4.9.jar) to field java.util.TreeMap.comparator
WARNING: Please consider reporting this to the maintainers of com.thoughtworks.xstream.core.util.Fields
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Quitting from lines 183-187 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
Assigned data `paste(seq(as.numeric(lowerRange), as.numeric(upperRange)), collapse = ",")` must be compatible with existing data.
ℹ Error occurred for column `Indices`.
✖ No common type for `value` <character> and `x` <double>.
--- failed re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [5s/9s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > # Modeled after the R6 testing structure: https://github.com/wch/R6/blob/master/tests/testthat.R
  > library(testthat)
  > library(REDCapR)
  > 
  > testthat::test_check("REDCapR")
  ── 1. Failure: validate_no_logical -concern dataset (@test-validate.R#36)  ─────
  ds$field_index not equal to 2.
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 135 | SKIPPED: 79 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: validate_no_logical -concern dataset (@test-validate.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:1: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rggobi.Rcheck/00install.out’ for details.
Found the following significant warnings:
   #warning "The <sys/sysctl.h> header is deprecated and will be removed."
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RhpcBLASctl.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(riskclustr)
  > 
  > test_check("riskclustr")
  ── 1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_message(...)
    6. riskclustr::optimal_kmeans_d(...)
    7. base::lapply(...)
    8. riskclustr:::FUN(X[[i]], ...)
    9. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   12. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   13. tibble:::tbl_subset_row(xo, i = i, i_arg)
   14. tibble:::vectbl_as_row_index(i, x, i_arg)
   15. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   22. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ── 2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_equal(...)
    4. riskclustr::optimal_kmeans_d(...)
    5. base::lapply(...)
    6. riskclustr:::FUN(X[[i]], ...)
    7. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   10. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   11. tibble:::tbl_subset_row(xo, i = i, i_arg)
   12. tibble:::vectbl_as_row_index(i, x, i_arg)
   13. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   20. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 26 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_kmeans_d.R#49) 
  2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_kmeans_d.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’

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:
  Rserv.c:2150:3: warning: ‘RSA_generate_key’ is deprecated [-Wdeprecated-declarations]
  Rserv.c:816:4: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:817:3: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:820:22: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:821:22: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:372:2: warning: ignoring return value of ‘chown’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:375:3: warning: ignoring return value of ‘chown’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2342:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:3351:4: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:3358:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2088:7: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2090:7: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  oc.c:47:5: warning: ‘RAND_pseudo_bytes’ is deprecated [-Wdeprecated-declarations]
  standalone.c:220:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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 notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(simrel)
  > 
  > test_check("simrel")
  ── 1. Error: Prepare Design (@test-utils.R#44)  ────────────────────────────────
  Can't join on 'q' x 'q' because of incompatible types (list / list)
  Backtrace:
   1. testthat::expect_identical(prepare_design(opts), dgn)
   3. testthat:::compare.default(act$val, exp$val)
   5. dplyr:::all.equal.tbl_df(x, y, ...)
   6. dplyr:::equal_data_frame(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 169 | SKIPPED: 21 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: Prepare Design (@test-utils.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/SpatialPosition.Rcheck/00install.out’ for details.
Running examples in ‘spatial.tools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tahoe_highrez_training
> ### Title: Point and polygon files for use with spatial.tools
> ### Aliases: tahoe_highrez_training
> ### Keywords: data
> 
> ### ** Examples
> 
> library("raster")
Loading required package: sp
> library("rgdal")
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 3.0.4, released 2020/01/28
 Path to GDAL shared files: 
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 7.0.0, March 1st, 2020, [PJ_VERSION: 700]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
> tahoe_highrez_training_polygons <- readOGR(
+ 	dsn=system.file("external", package="spatial.tools"),layer="tahoe_highrez_training")
OGR data source with driver: ESRI Shapefile 
Source: "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/spatial.tools/external", layer: "tahoe_highrez_training"
with 8 features
It has 2 fields
> spplot(tahoe_highrez_training_polygons,zcol="Class")
Warning in extend.limits(range(as.numeric(z), finite = TRUE)) :
  NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in seq.default(zrng[1], zrng[2], length.out = cuts + 2) : 
  'from' must be a finite number
Calls: spplot ... <Anonymous> -> levelplot.formula -> seq -> seq.default
Execution halted
Running ‘testthat.R’ [24s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #    Copyright 2015 Province of British Columbia
  > #
  > #    Licensed under the Apache License, Version 2.0 (the "License");
  > #    you may not use this file except in compliance with the License.
  > #    You may obtain a copy of the License at
  > #
  > #       http://www.apache.org/licenses/LICENSE-2.0
  > #
  > #    Unless required by applicable law or agreed to in writing, software
  > #    distributed under the License is distributed on an "AS IS" BASIS,
  > #    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  > #    See the License for the specific language governing permissions and
  > #    limitations under the License.
  > 
  > library(testthat)
  > library(ssdtools)
  
  Attaching package: 'ssdtools'
  
  The following objects are masked from 'package:stats':
  
      dgamma, dweibull, pgamma, pweibull, qgamma, qweibull, rgamma,
      rweibull
  
  > 
  > test_check("ssdtools")
  ── 1. Failure: ssd_gof fitdistscens (@test-gof.R#46)  ──────────────────────────
  as.data.frame(ssd_gof(fluazinam_dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ── 2. Failure: manual (@test-schwarz-tillmans.R#24)  ───────────────────────────
  as.data.frame(ssd_gof(dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 269 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 2 ]
  1. Failure: ssd_gof fitdistscens (@test-gof.R#46) 
  2. Failure: manual (@test-schwarz-tillmans.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/tanaka.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [27s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(taxa)
  
  Attaching package: 'taxa'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("taxa")
  ── 1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 607 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#52) 
  2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#56) 
  3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.R’ [4s/15s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library("taxize")
  > test_check("taxize")
  taxize options
    taxon_state_messages: TRUE
  ── 1. Failure: fails well (@test-tol_resolve.R#56)  ────────────────────────────
  `tol_resolve(context_name = "stuff")` threw an error with unexpected message.
  Expected match: "is not valid"
  Actual message: "Timeout was reached: [api.opentreeoflife.org] Connection timed out after 10000 milliseconds"
  Backtrace:
    1. testthat::expect_error(tol_resolve(context_name = "stuff"), "is not valid")
    6. taxize::tol_resolve(context_name = "stuff")
    7. rotl::tnrs_match_names(...)
   10. rotl::tnrs_contexts(...)
   11. rotl:::.tnrs_contexts(...)
   12. rotl:::otl_POST("tnrs/contexts", body = list(), ...)
   13. httr::POST(...)
   14. httr:::request_perform(req, hu$handle$handle)
   16. httr:::request_fetch.write_memory(req$output, req$url, handle)
   17. curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 52 | SKIPPED: 207 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: fails well (@test-tol_resolve.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/terra.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [17s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  ── 1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15)  ────
  paste(as.character(ovid[[1]]), collapse = " ") not equal to td$text[1].
  names for current but not for target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 297 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/tolBasis.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/tricolore.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # load packages
  > library(testthat)
  > library(wdpar)
  Loading required package: sf
  Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 7.0.0
  > 
  > # enable parallel testing
  > Sys.unsetenv("R_TESTS")
  > 
  > # run tests
  > test_check("wdpar")
  ── 1. Error: st_erase_overlaps (sf)  ───────────────────────────────────────────
  'st_make_valid' is not an exported object from 'namespace:lwgeom'
  Backtrace:
   1. wdpar::st_erase_overlaps(x)
   7. lwgeom::st_make_valid
   8. base::getExportedValue(pkg, name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 9 | SKIPPED: 14 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: st_erase_overlaps (sf) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘lubridate::intersect’ by ‘raster::intersect’ when loading ‘xROI’
  Warning: replacing previous import ‘lubridate::union’ by ‘raster::union’ when loading ‘xROI’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/xROI.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘zoomgrid-vignette.Rmd’ using rmarkdown
Could not fetch https://latex.codecogs.com/gif.latex?f%28x_1%2C%20x_2%29%20%3D%202%20A%20+%20%5Csum_%7Bi%3D1%7D%5E2%20%5Cleft%28%20x_i%5E2%20-%20A%20%5Ccos%282%20%5Cpi%20x_i%29%20%5Cright%29
HttpExceptionRequest Request {
  host                 = "latex.codecogs.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/gif.latex"
  queryString          = "?f%28x_1%2C%20x_2%29%20%3D%202%20A%20+%20%5Csum_%7Bi%3D1%7D%5E2%20%5Cleft%28%20x_i%5E2%20-%20A%20%5Ccos%282%20%5Cpi%20x_i%29%20%5Cright%29"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ConnectionTimeout
Error: processing vignette 'zoomgrid-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘zoomgrid-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘aaSEA_Documentation.Rmd’ using rmarkdown
Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

[WARNING] Could not parse YAML metadata at line 14 column 1: not an object
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘aaSEA_Documentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ABACUS.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ABACUS.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ABACUS.Rmd’

--- re-building ‘ABACUS_activities.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ABACUS_activities.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ABACUS_activities.Rmd’

SUMMARY: processing the following files failed:
  ‘ABACUS.Rmd’ ‘ABACUS_activities.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘example.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'example.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘example.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘overview.Rmd’

--- re-building ‘wiscads.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'wiscads.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘wiscads.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ABHgenotypeR-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ABHgenotypeR-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ABHgenotypeR-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘accelerometry.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'accelerometry.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘accelerometry.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Packages required but not available: 'aroma.affymetrix', 'aroma.core'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘ACSN-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ACSN-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ACSN-vignette.Rmd’

--- re-building ‘ACSN_map_updating.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ACSN_map_updating.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ACSN_map_updating.Rmd’

SUMMARY: processing the following files failed:
  ‘ACSN-vignette.Rmd’ ‘ACSN_map_updating.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ActFrag.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ActFrag.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ActFrag.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘actuaryr-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'actuaryr-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘actuaryr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ADAPRVignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ADAPRVignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ADAPRVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘AdaptGauss.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'AdaptGauss.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘AdaptGauss.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘adaptive_gpca_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'adaptive_gpca_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘adaptive_gpca_vignette.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Running ‘add.R’ [9s/12s]
  Running ‘adegraphics.R’ [3s/4s]
  Running ‘nbgraph.R’ [3s/4s]
Running the tests in ‘tests/nbgraph.R’ failed.
Last 13 lines of output:
      kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
      s.label, s.logo, s.match, s.traject, s.value, table.value,
      triangle.class
  
  > library(spdep)
  Loading required package: sp
  Loading required package: spData
  To access larger datasets in this package, install the spDataLarge
  package with: `install.packages('spDataLarge',
  repos='https://nowosad.github.io/drat/', type='source')`
  Loading required package: sf
  Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0
  Error: package or namespace load failed for 'spdep' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
   there is no package called 'expm'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘adepro.rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'adepro.rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘adepro.rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘adept-intro.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'adept-intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘adept-intro.Rmd’

--- re-building ‘adept-strides-segmentation.Rmd’ using rmarkdown

Attaching package: 'lubridate'

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

    date


Attaching package: 'dplyr'

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

    intersect, setdiff, union

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'adept-strides-segmentation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘adept-strides-segmentation.Rmd’

SUMMARY: processing the following files failed:
  ‘adept-intro.Rmd’ ‘adept-strides-segmentation.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘AdhereR-overview.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'AdhereR-overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘AdhereR-overview.Rmd’

--- re-building ‘calling-AdhereR-from-python3.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'calling-AdhereR-from-python3.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘calling-AdhereR-from-python3.Rmd’

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

SUMMARY: processing the following files failed:
  ‘AdhereR-overview.Rmd’ ‘calling-AdhereR-from-python3.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘HiTC’
Package unavailable to check Rd xrefs: ‘HiTC’
Error(s) in re-building vignettes:
  ...
--- re-building ‘admixturegraph.Rmd’ using rmarkdown
Loading required package: optimbase
Loading required package: Matrix
Loading required package: optimsimplex
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'admixturegraph.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘admixturegraph.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘adnuts.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'adnuts.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘adnuts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘vdiffr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ADPclust.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ADPclust.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ADPclust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advclust.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'advclust.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘advclust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘About.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'About.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘About.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/AGread.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'gge', 'SpATS'
Error(s) in re-building vignettes:
  ...
--- re-building ‘agridat_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.
--- finished re-building ‘agridat_data.Rmd’

--- re-building ‘agridat_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 40-49 (agridat_examples.Rmd) 
Error: processing vignette 'agridat_examples.Rmd' failed with diagnostics:
there is no package called 'gge'
--- failed re-building ‘agridat_examples.Rmd’

--- re-building ‘agridat_papadakis.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 ‘agridat_papadakis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_the_AHM_package.Rmd’ using rmarkdown
Loading required package: quadprog
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 3.0-2

Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

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

    nobs

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

    object.size

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

    startsWith

Loading required package: lattice
Loading required package: grid
Loading required package: daewr
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction_to_the_AHM_package.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Introduction_to_the_AHM_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ahn.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ahn.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ahn.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘examples.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘examples.Rmd’

--- re-building ‘file-format.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'file-format.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘file-format.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'R2jags', 'jagsUI'
Error(s) in re-building vignettes:
--- re-building ‘get_started.rmd’ using rmarkdown
Warning in CreateRunOptions(FUN_MOD = get(PrepGR$TypeModel), InputsModel = PrepGR$InputsModel,  :
  model warm up period not defined: default configuration used
  the year preceding the run period is used 

Warning in CreateRunOptions(FUN_MOD = get(PrepGR$TypeModel), InputsModel = PrepGR$InputsModel,  :
  model warm up period not defined: default configuration used
  the year preceding the run period is used 

Warning in plot.OutputsModel(x$OutputsModel, Qobs = x$Qobs, ...) :
  zeroes detected in 'Qsim': some plots in the log space will not be created using all time-steps
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'get_started.rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘get_started.rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_Airportr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction_to_Airportr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Introduction_to_Airportr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Usage-Vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Usage-Vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Usage-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Usage-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘akc_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'akc_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘akc_vignette.Rmd’

--- re-building ‘tutorial_raw_text.Rmd’ using rmarkdown
Warning in wordcloud_boxes(data_points = points_valid_first, boxes = boxes,  :
  Some words could not fit on page. They have been placed at their original positions.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'tutorial_raw_text.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘tutorial_raw_text.Rmd’

SUMMARY: processing the following files failed:
  ‘akc_vignette.Rmd’ ‘tutorial_raw_text.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘akmedoids-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'akmedoids-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘akmedoids-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ALA4R.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: maps
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-6

Attaching package: 'vegan'

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

    scores

Warning: Removed 4 rows containing missing values (geom_point).
Warning in FUN(X[[i]], ...) :
  No images were found for occurrence id e735985d-ec69-4f39-974e-71f16787b274
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ALA4R.Rmd’

SUMMARY: processing the following file failed:
  ‘ALA4R.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘alfred.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'alfred.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘alfred.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘working_with_content.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'working_with_content.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘working_with_content.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-algorithmia.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction-to-algorithmia.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction-to-algorithmia.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘allelic/libs/allelic.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘allestimates-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'allestimates-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘allestimates-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘alphabetr-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'alphabetr-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘alphabetr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘alphapart-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'alphapart-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘alphapart-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
Error(s) in re-building vignettes:
--- re-building ‘intro.Rmd’ using rmarkdown
Loading required package: R6
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘intro.Rmd’

--- re-building ‘traits.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'traits.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘traits.Rmd’

SUMMARY: processing the following files failed:
  ‘intro.Rmd’ ‘traits.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘AlphaVantageClient.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'AlphaVantageClient.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘AlphaVantageClient.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_alterryx.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'using_alterryx.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘using_alterryx.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘amen.Rnw’ using knitr
Loading required package: network
network: Classes for Relational Data
Version 1.16.0 created on 2019-11-30.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
Fontconfig error: Cannot load default config file
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- 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 ‘ampir.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ampir.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ampir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘anchoredDistr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'anchoredDistr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘anchoredDistr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘creel_survey_simulation.Rmd’ using rmarkdown
      Ehat
1 897.1823
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'creel_survey_simulation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘creel_survey_simulation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘anipaths.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'anipaths.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘anipaths.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    24.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_ANOVAreplication.Rmd’ using rmarkdown_notangle
Loading required package: quadprog
Loading required package: shiny
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'vignette_ANOVAreplication.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘vignette_ANOVAreplication.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘antaresEditObject.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'antaresEditObject.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘antaresEditObject.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘antaresProcessing.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'antaresProcessing.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘antaresProcessing.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘antaresH5.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘antaresH5.Rmd’

--- re-building ‘antaresRead.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'antaresRead.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘antaresRead.Rmd’

SUMMARY: processing the following files failed:
  ‘antaresH5.Rmd’ ‘antaresRead.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘antaresViz.Rmd’ using rmarkdown
Loading required package: antaresRead
Loading required package: antaresProcessing
Loading required package: spMaps
Loading required package: sp
Loading required package: raster

Attaching package: 'raster'

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

    getValues

Loading required package: rgeos
rgeos version: 0.5-2, (SVN revision 621)
 GEOS runtime version: 3.7.2-CAPI-1.11.2 
 Linking to sp version: 1.4-1 
 Polygon checking: TRUE 

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'antaresViz.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘antaresViz.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_AnthropMMD.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'intro_AnthropMMD.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘intro_AnthropMMD.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ── 2. Failure: Type with VIRTUAL (@test-S4-types.R#111)  ───────────────────────
  names(Test(x = 2)) == "x" isn't true.
  
  ── 3. Failure: Type with VIRTUAL (@test-S4-types.R#112)  ───────────────────────
  inherits(Test(), "Type") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 187 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Type inheritance (@test-S4-types.R#75) 
  2. Failure: Type with VIRTUAL (@test-S4-types.R#111) 
  3. Failure: Type with VIRTUAL (@test-S4-types.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- 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 ‘apaTables.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'apaTables.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘apaTables.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 157.6Mb
  sub-directories of 1Mb or more:
    libs  157.1Mb
Package suggested but not available for checking: ‘kebabs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘apcluster.Rnw’ using knitr

Attaching package: 'apcluster'

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

    heatmap

Quitting from lines 387-408 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres2c' not found
--- failed re-building ‘apcluster.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [7s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  subscript out of bounds
  Backtrace:
   1. apex::multidna2genind(x, mlst = TRUE, gapIsNA = TRUE)
   2. adegenet::df2genind(xdfnum, ploidy = 1, ind.names = x@labels)
   3. base::vapply(...)
   4. adegenet:::FUN(X[[i]], ...)
   5. base::rowSums(out[, i, drop = FALSE], na.rm = TRUE)
   6. base::is.data.frame(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 1 ]
  1. Error: (unknown) (@test_export.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘apex.Rmd’ using rmarkdown
Quitting from lines 294-299 (apex.Rmd) 
Error: processing vignette 'apex.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘apex.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘aphid-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'aphid-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘aphid-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘APIS_vignette.Rmd’ using rmarkdown
WARNING! Your marker set is not enough powerfull!
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'APIS_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘APIS_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ggtree’
Running examples in ‘aplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: insert_left
> ### Title: plot-insertion
> ### Aliases: insert_left insert_right insert_top insert_bottom
> 
> ### ** Examples
> 
> library(ggplot2)
> library(aplot)
> 
> p <- ggplot(mtcars, aes(mpg, disp)) + geom_point()
> p2 <- ggplot(mtcars, aes(mpg)) + 
+     geom_density(fill='steelblue', alpha=.5) + 
+         ggtree::theme_dendrogram()
Error in loadNamespace(name) : there is no package called ‘ggtree’
Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘aroma.light’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘apollofirstexample.Rmd’ using rmarkdown
Apollo ignition sequence completed
Warning in sink() : no sink to remove
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'apollofirstexample.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘apollofirstexample.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'RGtk2', 'gWidgetsRGtk2', 'cairoDevice'
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/aqr.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘AQuadtreeUse.Rmd’ using rmarkdown
layer:1

layer:2

layer:1

layer:2

layer:3

layer:4

layer:1

layer:2

layer:3

layer:4

layer:1

layer:2

layer:3

layer:4

layer:1

layer:2

layer:3

layer:4

layer:5

layer:1

layer:2

layer:3

layer:4

layer:5

layer:1

layer:2

layer:3

layer:4

layer:5

layer:1

layer:2

layer:3

layer:4

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'AQuadtreeUse.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘AQuadtreeUse.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘CombinationOfGaussianDates.Rmd’ using rmarkdown
Loading required package: coda
Loading required package: rjags
Linked to JAGS 4.3.0
Loaded modules: basemod,bugs
Loading required package: ArchaeoPhases
Loading required package: hdrcde
This is hdrcde 3.3
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'CombinationOfGaussianDates.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CombinationOfGaussianDates.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘rgl’
Error(s) in re-building vignettes:
  ...
--- re-building ‘archivist_and_GitHub_integration.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'archivist_and_GitHub_integration.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘archivist_and_GitHub_integration.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘areal-weighted-interpolation.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'areal-weighted-interpolation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘areal-weighted-interpolation.Rmd’

--- re-building ‘areal.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'areal.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘areal.Rmd’

--- re-building ‘data-preparation.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'data-preparation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘data-preparation.Rmd’

SUMMARY: processing the following files failed:
  ‘areal-weighted-interpolation.Rmd’ ‘areal.Rmd’ ‘data-preparation.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘arena2r-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'arena2r-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘arena2r-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘arena2r-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘argparse.Rrst’ using knitr
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
--- failed re-building ‘argparse.Rrst’

SUMMARY: processing the following file failed:
  ‘argparse.Rrst’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Simple-Ari-Configuration-with-Docker.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Simple-Ari-Configuration-with-Docker.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Simple-Ari-Configuration-with-Docker.Rmd’

SUMMARY: processing the following file failed:
  ‘Simple-Ari-Configuration-with-Docker.Rmd’

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

Packages suggested but not available for checking:
  'affxparser', 'aroma.light', 'oligo', 'oligoClasses',
  'pdInfoBuilder', 'AffymetrixDataTestFiles'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Packages required but not available: 'aroma.core', 'PSCBS'

Packages suggested but not available for checking: 'aroma.light', 'GLAD'

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

Packages suggested but not available for checking:
  'aroma.light', 'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    libs  34.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘aRxiv.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'aRxiv.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘aRxiv.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘adaptive_shrinkage.Rmd’ using rmarkdown
Warning: Removed 1274 rows containing missing values (geom_point).
Warning: Removed 1274 rows containing missing values (geom_point).
Warning: Removed 89 rows containing missing values (geom_point).
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'adaptive_shrinkage.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘adaptive_shrinkage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘assertr.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'assertr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘assertr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘AssetCorr_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'AssetCorr_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘AssetCorr_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘asymmetry.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'asymmetry.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘asymmetry.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘atsd_package.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'atsd_package.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘atsd_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fill-pkg-description.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'fill-pkg-description.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘fill-pkg-description.Rmd’

SUMMARY: processing the following file failed:
  ‘fill-pkg-description.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-auctestr-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'basic-auctestr-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘basic-auctestr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  au.c:222:8: warning: 'AudioHardwareGetProperty' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  au.c:229:8: warning: 'AudioDeviceGetProperty' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  au.c:375:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int)') with an expression of type 'au_instance_t *(SEXP, float, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int)') [-Wincompatible-pointer-types]
  au.c:376:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int, int)') with an expression of type 'au_instance_t *(SEXP, float, int, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int, int)') [-Wincompatible-pointer-types]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/audio.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’ using rmarkdown_notangle
trying URL 'https://www.r-project.org/logo/Rlogo.png'
Content type 'image/png' length 48148 bytes (47 KB)
==================================================
downloaded 47 KB

trying URL 'https://raw.githubusercontent.com/aravind-j/augmentedRCBD/master/vignettes/rbase.png'
Content type 'image/png' length 57299 bytes (55 KB)
==================================================
downloaded 55 KB

trying URL 'https://github.com/aravind-j/augmentedRCBD/raw/master/vignettes/rstudio.png'
Content type 'image/png' length 91730 bytes (89 KB)
==================================================
downloaded 89 KB

trying URL 'https://github.com/aravind-j/augmentedRCBD/raw/master/vignettes/rstudio%20panes.png'
Content type 'image/png' length 86653 bytes (84 KB)
==================================================
downloaded 84 KB

Fontconfig error: Cannot load default config file
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Data_Analysis_with_augmentedRCBD.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘auk.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'auk.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘auk.Rmd’

--- re-building ‘development.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'development.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘development.Rmd’

SUMMARY: processing the following files failed:
  ‘auk.Rmd’ ‘development.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘basic-usage.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘basic-usage.Rmd’

--- re-building ‘migration-to-new-syntax.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'migration-to-new-syntax.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘migration-to-new-syntax.Rmd’

SUMMARY: processing the following files failed:
  ‘basic-usage.Rmd’ ‘migration-to-new-syntax.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette-html.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'vignette-html.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘vignette-html.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘AutoDeskR.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'AutoDeskR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘AutoDeskR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Error(s) in re-building vignettes:
--- re-building ‘autoimage.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'autoimage.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘autoimage.Rmd’

--- re-building ‘autopoints.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'autopoints.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘autopoints.Rmd’

--- re-building ‘ggplot2-comparison.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ggplot2-comparison.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ggplot2-comparison.Rmd’

SUMMARY: processing the following files failed:
  ‘autoimage.Rmd’ ‘autopoints.Rmd’ ‘ggplot2-comparison.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'siggenes', 'fgsea', 'org.Hs.eg.db', 'ConsensusClusterPlus',
  'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘avar-example.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'avar-example.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘avar-example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘full-example.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'full-example.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘full-example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- 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 ‘shiny.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'shiny.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘shiny.Rmd’

--- re-building ‘token.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'token.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘token.Rmd’

SUMMARY: processing the following files failed:
  ‘shiny.Rmd’ ‘token.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vig01_plumber_deploy.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'vig01_plumber_deploy.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘vig01_plumber_deploy.Rmd’

--- re-building ‘vig02_mmls_deploy.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'vig02_mmls_deploy.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘vig02_mmls_deploy.Rmd’

--- re-building ‘vig03_rbac.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'vig03_rbac.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘vig03_rbac.Rmd’

SUMMARY: processing the following files failed:
  ‘vig01_plumber_deploy.Rmd’ ‘vig02_mmls_deploy.Rmd’ ‘vig03_rbac.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘AzureKusto.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'AzureKusto.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘AzureKusto.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘configuration.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'configuration.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘configuration.Rmd’

--- re-building ‘installation.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'installation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘installation.Rmd’

SUMMARY: processing the following files failed:
  ‘configuration.Rmd’ ‘installation.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘generics.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'generics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘generics.Rmd’

--- re-building ‘intro.rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'intro.rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘intro.rmd’

SUMMARY: processing the following files failed:
  ‘generics.Rmd’ ‘intro.rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘computervision.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'computervision.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘computervision.Rmd’

--- re-building ‘customvision.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'customvision.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘customvision.Rmd’

SUMMARY: processing the following files failed:
  ‘computervision.Rmd’ ‘customvision.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'intro.rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘intro.rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Price_and_Index_Reports.Rmd’ using rmarkdown
trying URL 'http://www.b3.com.br/pesquisapregao/download?filelist=IR190918.zip'
downloaded 6691 bytes

Warning in in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,  :
  You changed the working directory to /private/var/folders/08/nc4f1s3x1jqd9ln5mnvrqzqh0000gp/T/RtmpE7uiPb (probably via setwd()). It will be restored to /Volumes/Builds/packages/high-sierra-x86_64/results/4.0/b3archives.Rcheck/vign_test/b3archives/vignettes. See the Note section in ?knitr::knit
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Price_and_Index_Reports.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Price_and_Index_Reports.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘exampleBackShift.Rmd’ using rmarkdown
Loading required package: backShift
Loading required package: ggplot2
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.5-1 (2019-12-12) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    backsolve, forwardsolve

Loading required package: maps
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
No id variables; using all as measure variables
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'exampleBackShift.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘exampleBackShift.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 67.7Mb
  sub-directories of 1Mb or more:
    libs  66.5Mb
Package suggested but not available for checking: ‘philr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘balance.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'balance.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘balance.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘use-ballr.Rmd’ using rmarkdown

Attaching package: 'janitor'

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

    chisq.test, fisher.test

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'use-ballr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘use-ballr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘rjags’
Package unavailable to check Rd xrefs: ‘rjags’
Error(s) in re-building vignettes:
--- re-building ‘CLI_guide.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'CLI_guide.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CLI_guide.Rmd’

--- re-building ‘quickstart.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘quickstart.Rmd’

SUMMARY: processing the following files failed:
  ‘CLI_guide.Rmd’ ‘quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'geocode.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘geocode.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ArrayExpress’
Error(s) in re-building vignettes:
--- re-building ‘Using-baRcodeR.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Using-baRcodeR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Using-baRcodeR.Rmd’

--- re-building ‘use-addin.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'use-addin.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘use-addin.Rmd’

SUMMARY: processing the following files failed:
  ‘Using-baRcodeR.Rmd’ ‘use-addin.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- 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 ‘barplot3d.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'barplot3d.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘barplot3d.Rmd’

SUMMARY: processing the following file failed:
  ‘barplot3d.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   3.6Mb
Error(s) in re-building vignettes:
--- re-building ‘baRulho_quantifying_sound_degradation.Rmd’ using rmarkdown
Loading required package: warbleR
Loading required package: tuneR
Loading required package: seewave
Loading required package: NatureSounds
Loading required package: knitr

NOTE: functions are being renamed (run 'print(new_function_names)' to see new names). Both old and new names are available in this version 
 Please see citation('warbleR') for use in publication
Loading required package: viridisLite
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'baRulho_quantifying_sound_degradation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘baRulho_quantifying_sound_degradation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Error(s) in re-building vignettes:
--- re-building ‘base2grob.Rmd’ using rmarkdown

********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************

The base2grob package has been deprecated. Please switch over to the ggplotify package
Saving 7 x 5 in image
Saving 7 x 5 in image
Saving 7 x 5 in image
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'base2grob.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘base2grob.Rmd’

SUMMARY: processing the following file failed:
  ‘base2grob.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/baseflow.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘BASiNET.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'BASiNET.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘BASiNET.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘article2-vignette.Rnw’ using knitr

Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BatchGetSymbols-vignette.Rmd’ using rmarkdown
Warning in for (i in seq_along(members)) { :
  closing unused connection 5 (https://query1.finance.yahoo.com/v7/finance/download/abcdef?period1=1580601600&period2=1585785600&interval=1d&events=history&crumb=NJnm6vOlII4)
Warning in for (i in seq_along(members)) { :
  closing unused connection 4 (https://query2.finance.yahoo.com/v7/finance/download/abcdef?period1=1580601600&period2=1585785600&interval=1d&events=history&crumb=5KWF1mPVx0O)
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'BatchGetSymbols-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘BatchGetSymbols-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Error(s) in re-building vignettes:
  ...
--- re-building ‘BAwiR.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'BAwiR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘BAwiR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 53.3Mb
  sub-directories of 1Mb or more:
    libs  51.3Mb
Package required but not available: ‘mritc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/BAYESDEF.Rcheck/00install.out’ for details.
installed size is 54.2Mb
  sub-directories of 1Mb or more:
    libs  53.3Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  13.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BayesianNetwork.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'BayesianNetwork.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘BayesianNetwork.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘BayesianTools.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'BayesianTools.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘BayesianTools.Rmd’

--- re-building ‘InterfacingAModel.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'InterfacingAModel.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘InterfacingAModel.Rmd’

SUMMARY: processing the following files failed:
  ‘BayesianTools.Rmd’ ‘InterfacingAModel.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘PottsUtils’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BayesLogNormal.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'BayesLogNormal.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘BayesLogNormal.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BayesMallowsPackage.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'BayesMallowsPackage.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘BayesMallowsPackage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  18.4Mb
Error(s) in re-building vignettes:
--- re-building ‘graphical-ppcs.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'graphical-ppcs.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘graphical-ppcs.Rmd’

--- re-building ‘plotting-mcmc-draws.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'plotting-mcmc-draws.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘plotting-mcmc-draws.Rmd’

--- re-building ‘visual-mcmc-diagnostics.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'visual-mcmc-diagnostics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘visual-mcmc-diagnostics.Rmd’

SUMMARY: processing the following files failed:
  ‘graphical-ppcs.Rmd’ ‘plotting-mcmc-draws.Rmd’
  ‘visual-mcmc-diagnostics.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  13.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   3.5Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘bbw.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bbw.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bbw.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘bcdata.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bcdata.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bcdata.Rmd’

--- re-building ‘efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd’

SUMMARY: processing the following files failed:
  ‘bcdata.Rmd’
  ‘efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'R2jags', 'INLA'
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-the-BCHM-package.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'using-the-BCHM-package.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘using-the-BCHM-package.Rmd’

SUMMARY: processing the following file failed:
  ‘using-the-BCHM-package.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bchron.Rmd’ using rmarkdown
Warning: Removed 4940 row(s) containing missing values (geom_path).
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Bchron.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Bchron.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bclim.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Bclim.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Bclim.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BClustLonG.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'BClustLonG.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘BClustLonG.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘add_points.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'add_points.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘add_points.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘BRugs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'example.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bdl.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bdl.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bdl.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘reproduce_results.Rmd’ using rmarkdown
Loading required package: rmarkdown
Loading required package: shiny
Loading required package: shinyBS

BDP2 0.1.3 loaded.
Use BDP2workflow() for interactive shiny app, see 'help("BDP2-package")' and vignette for more information.

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'reproduce_results.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘reproduce_results.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bdscale.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bdscale.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bdscale.Rmd’

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

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

Packages suggested but not available for checking:
  'beadarrayExampleData', 'lumi'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 69.2Mb
  sub-directories of 1Mb or more:
    libs  67.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘beanz_vignettes.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'beanz_vignettes.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘beanz_vignettes.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘demo.Rmd’ using rmarkdown
Loading required package: beautier
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'demo.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘demo.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'demo.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘demo.Rmd’

--- re-building ‘examples.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘examples.Rmd’

SUMMARY: processing the following files failed:
  ‘demo.Rmd’ ‘examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using-bedr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Using-bedr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Using-bedr.Rmd’

SUMMARY: processing the following file failed:
  ‘Using-bedr.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘beezdemand.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'beezdemand.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘beezdemand.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘belg1.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'belg1.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘belg1.Rmd’

SUMMARY: processing the following file failed:
  ‘belg1.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘a_introduction.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'a_introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘a_introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘benthos.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

N_a(a=1) is undefined. Therefore N_a(lim a->1) will be returned
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'benthos.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘benthos.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘bestNormalize.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bestNormalize.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bestNormalize.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Using_betaboost_IJE.Rmd’ using rmarkdown
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
This is mboost 2.9-2. See 'package?mboost' and 'news(package  = "mboost")'
for a complete list of changes.

Loading required package: gamboostLSS

Attaching package: 'gamboostLSS'

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

    model.weights

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Using_betaboost_IJE.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Using_betaboost_IJE.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BetaPASS.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'BetaPASS.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘BetaPASS.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error: package or namespace load failed for ‘BETS’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so':
  dlopen(/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so, 6): Symbol not found: _GSS_C_NT_USER_NAME
  Referenced from: /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so
  Expected in: flat namespace
 in /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so
Execution halted
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so':
  dlopen(/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so, 6): Symbol not found: _GSS_C_NT_USER_NAME
  Referenced from: /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so
  Expected in: flat namespace
 in /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted

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: package or namespace load failed for ‘BETS’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so':
  dlopen(/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so, 6): Symbol not found: _GSS_C_NT_USER_NAME
  Referenced from: /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so
  Expected in: flat namespace
 in /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste("
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘BETS_basic_usage.Rmd’ using rmarkdown
Loading required package: BETS

Attaching package: 'BETS'

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

    predict

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'BETS_basic_usage.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘BETS_basic_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 131.4Mb
  sub-directories of 1Mb or more:
    include  131.3Mb
Error(s) in re-building vignettes:
--- re-building ‘bib2df.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: `cols` is now required.
Please use `cols = c(AUTHOR)`
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bib2df.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bib2df.Rmd’

SUMMARY: processing the following file failed:
  ‘bib2df.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘bibliometrix-vignette.Rmd’ using rmarkdown
Warning: Use of `A$dim1` is discouraged. Use `dim1` instead.
Warning: Use of `A$dim2` is discouraged. Use `dim2` instead.
Warning: Use of `A$nomi` is discouraged. Use `nomi` instead.
Warning: Use of `A$dim1` is discouraged. Use `dim1` instead.
Warning: Use of `A$dim2` is discouraged. Use `dim2` instead.
Warning: Use of `A$nomi` is discouraged. Use `nomi` instead.
Warning: Use of `B$dim1` is discouraged. Use `dim1` instead.
Warning: Use of `B$dim2` is discouraged. Use `dim2` instead.
Warning: Use of `B$nomi` is discouraged. Use `nomi` instead.
Warning: Use of `B$dim1` is discouraged. Use `dim1` instead.
Warning: Use of `B$dim2` is discouraged. Use `dim2` instead.
Warning: Use of `B$nomi` is discouraged. Use `nomi` instead.
Warning: The curvature argument has been deprecated in favour of strength
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bibliometrix-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bibliometrix-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.8Mb
Error(s) in re-building vignettes:
--- re-building ‘BIGDAWG.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'BIGDAWG.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘BIGDAWG.Rmd’

--- re-building ‘GLSconvert.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'GLSconvert.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘GLSconvert.Rmd’

SUMMARY: processing the following files failed:
  ‘BIGDAWG.Rmd’ ‘GLSconvert.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Package suggested but not available for checking: ‘RODBC’
Error(s) in re-building vignettes:
--- re-building ‘analysis.Rmd’ using rmarkdown
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'analysis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘analysis.Rmd’

--- re-building ‘methodology.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'methodology.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘methodology.Rmd’

SUMMARY: processing the following files failed:
  ‘analysis.Rmd’ ‘methodology.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rmpi’
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bigmemory)
  > 
  > test_check("bigmemory")
  Error in loadNamespace(name) : there is no package called 'cli'
  Calls: test_check ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bigQueryR.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bigQueryR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bigQueryR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      8.6Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/bild.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/bimetallic.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/bimets.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘binman-Basics.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'binman-Basics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘binman-Basics.Rmd’

SUMMARY: processing the following file failed:
  ‘binman-Basics.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  boot_dist.cpp:117:5: warning: ignoring return value of function declared with const attribute [-Wunused-value]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/binnednp.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘binomialMix.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'binomialMix.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘binomialMix.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘binocular_visual_field.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'binocular_visual_field.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘binocular_visual_field.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   2.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/bioacoustics.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘BioCircos.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 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘BioCircos.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'BiocStyle', 'BiocVersion'
Error(s) in re-building vignettes:
--- re-building ‘case-study.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'case-study.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘case-study.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following files failed:
  ‘case-study.Rmd’ ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Loading required package: slam
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- 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 ‘readwriteplot.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'readwriteplot.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘readwriteplot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘inactivation.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'inactivation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘inactivation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bioi.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Bioi.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Bioi.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error: package or namespace load failed for ‘biolink’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so':
  dlopen(/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so, 6): Symbol not found: _GSS_C_NT_USER_NAME
  Referenced from: /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so
  Expected in: flat namespace
 in /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so
Execution halted
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so':
  dlopen(/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so, 6): Symbol not found: _GSS_C_NT_USER_NAME
  Referenced from: /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so
  Expected in: flat namespace
 in /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted

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: package or namespace load failed for ‘biolink’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so':
  dlopen(/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so, 6): Symbol not found: _GSS_C_NT_USER_NAME
  Referenced from: /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so
  Expected in: flat namespace
 in /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RMySQL/libs/RMySQL.so
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           past
Execution halted
Packages required but not available: 'ChemmineR', 'fmcsR', 'org.Hs.eg.db'

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

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

Package suggested but not available for checking: ‘soilphysics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘colorspace’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘deldir’ ‘rgl’ ‘tcltk’ ‘tcltk2’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error(s) in re-building vignettes:
  ...
--- re-building ‘biscale.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'biscale.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘biscale.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘org.Hs.eg.db’
Errors in running code in vignettes:
when running code in ‘BiSEp.Snw’
  ...
+     mutationGene = "PBRM1")

> waterfallPlot(BISEP_data, MUT_data, expressionGene = "BOK", 
+     mutationGene = "BRCA2")

> fOut <- FURE(BIGEE_out[1, ], inputType = "BIGEE")

  When sourcing ‘BiSEp.R’:
Error: there is no package called ‘org.Hs.eg.db’
Execution halted

  ‘BiSEp.Snw’... failed
Error(s) in re-building vignettes:
--- re-building ‘BiSEp.Snw’ using Sweave
Loading required package: BiSEp
Loading required package: mclust
Package 'mclust' version 5.4.5
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: GOSemSim

GOSemSim v2.13.1  For help: https://guangchuangyu.github.io/GOSemSim

If you use GOSemSim in published research, please cite:
[36m-[39m Guangchuang Yu. Gene Ontology Semantic Similarity Analysis Using GOSemSim. In: Kidder B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, 2020, 2117:207-215. Humana, New York, NY. doi:10.1007/978-1-0716-0301-7_11
[36m-[39m Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics 2010, 26(7):976-978. doi:10.1093/bioinformatics/btq064



Error: processing vignette 'BiSEp.Snw' failed with diagnostics:
 chunk 16 (label = packages) 
Error in loadNamespace(name) : there is no package called ‘org.Hs.eg.db’

--- failed re-building ‘BiSEp.Snw’

SUMMARY: processing the following file failed:
  ‘BiSEp.Snw’

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Error(s) in re-building vignettes:
--- re-building ‘BIS.Rmd’ using rmarkdown
Parsed with column specification:
cols(
  .default = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  .default = col_double(),
  FREQ = col_character(),
  Frequency = col_character(),
  REF_AREA = col_character(),
  `Reference area` = col_character(),
  `Time Period` = col_character()
)
See spec(...) for full column specifications.

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: 'zoo'

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

    as.Date, as.Date.numeric

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'BIS.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘BIS.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘IHW’
Package suggested but not available for checking: ‘mrfDepth’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_blaise.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction_to_blaise.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction_to_blaise.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [5s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    Expected in: /usr/lib/libSystem.B.dylib
  
  ── 1. Error: knitr_sidecar_prefix preconditions hold (@test-utils.R#12)  ───────
  pandoc document conversion failed with error 6
  Backtrace:
   1. rmarkdown::render(rmd_path, quiet = TRUE)
   2. rmarkdown:::convert(output_file, run_citeproc)
   3. rmarkdown::pandoc_convert(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 190 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: knitr_sidecar_prefix preconditions hold (@test-utils.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘sending_using_smtp.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'sending_using_smtp.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘sending_using_smtp.Rmd’

--- re-building ‘simple_composition.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'simple_composition.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘simple_composition.Rmd’

SUMMARY: processing the following files failed:
  ‘sending_using_smtp.Rmd’ ‘simple_composition.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 53.5Mb
  sub-directories of 1Mb or more:
    libs  51.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘blkbox_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'blkbox_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘blkbox_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  32.8Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_BMRSr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'using_BMRSr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘using_BMRSr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [14s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("BMTME")
  ── 1. Failure: RandomPartition (@test.R#52)  ───────────────────────────────────
  RP_Test$Environments inherits from `character` not `factor`.
  
  ── 2. Failure: RandomPartition (@test.R#72)  ───────────────────────────────────
  RP_Test2$Traits inherits from `character` not `factor`.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 143 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: RandomPartition (@test.R#52) 
  2. Failure: RandomPartition (@test.R#72) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Error(s) in re-building vignettes:
--- re-building ‘bnspatial.Rmd’ using rmarkdown
Loading required package: raster
Loading required package: sp
  FinalLULC cell_ID
1    forest       1
2    arable       2
3     other       3
  FinalLULC cell_ID
1    forest       1
2    arable       2
3     other       3
  RelativePreference cell_ID
1             forest       1
2             arable       2
3              other       3
  RelativePreference cell_ID
1             forest       1
2             arable       2
3              other       3
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bnspatial.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bnspatial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘sangerseqR’
Error(s) in re-building vignettes:
--- re-building ‘bomrang.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bomrang.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bomrang.Rmd’

--- re-building ‘use_case.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'use_case.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘use_case.Rmd’

SUMMARY: processing the following files failed:
  ‘bomrang.Rmd’ ‘use_case.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 335.1Mb
  sub-directories of 1Mb or more:
    include    8.5Mb
    lib      326.3Mb
installed size is 75.7Mb
  sub-directories of 1Mb or more:
    libs  75.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Error(s) in re-building vignettes:
  ...
--- re-building ‘brainKCCA.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'brainKCCA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘brainKCCA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘data_formats.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'data_formats.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘data_formats.Rmd’

--- re-building ‘methods_and_concepts.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'methods_and_concepts.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘methods_and_concepts.Rmd’

SUMMARY: processing the following files failed:
  ‘data_formats.Rmd’ ‘methods_and_concepts.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
Packages suggested but not available for checking:
  'R2jags', 'rjags', 'runjags'
Error(s) in re-building vignettes:
--- re-building ‘brinton.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'brinton.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘brinton.Rmd’

--- re-building ‘specimen.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'specimen.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘specimen.Rmd’

SUMMARY: processing the following files failed:
  ‘brinton.Rmd’ ‘specimen.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘available_methods.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'broom'

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

    augment, glance, tidy


Attaching package: 'broom.mixed'

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

    tidyMCMC

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

    augment, glance, tidy

Joining, by = "class"
Joining, by = "class"
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'available_methods.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘available_methods.Rmd’

--- re-building ‘tests_and_coverage.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'tests_and_coverage.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘tests_and_coverage.Rmd’

SUMMARY: processing the following files failed:
  ‘available_methods.Rmd’ ‘tests_and_coverage.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'glmmADMB', 'R2jags'
Error(s) in re-building vignettes:
--- re-building ‘broom_mixed_intro.rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Registered S3 methods overwritten by 'broom.mixed':
  method         from 
  augment.lme    broom
  augment.merMod broom
  glance.lme     broom
  glance.merMod  broom
  glance.stanreg broom
  tidy.brmsfit   broom
  tidy.gamlss    broom
  tidy.lme       broom
  tidy.merMod    broom
  tidy.rjags     broom
  tidy.stanfit   broom
  tidy.stanreg   broom
Loading required package: brms
Loading required package: Rcpp
Loading 'brms' package (version 2.12.0). Useful instructions
can be found by typing help('brms'). A more detailed introduction
to the package is available through vignette('brms_overview').

Attaching package: 'brms'

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

    ar

Loading required package: dotwhisker
Loading required package: ggplot2
Loading required package: pander
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'broom_mixed_intro.rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘broom_mixed_intro.rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'btergm', 'xergm'
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘pasilla’
Error(s) in re-building vignettes:
  ...
--- re-building ‘brt.rmd’ using rmarkdown
Quitting from lines 134-143 (brt.rmd) 
Error: processing vignette 'brt.rmd' failed with diagnostics:
With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install
--- failed re-building ‘brt.rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  28.4Mb
installed size is 93.9Mb
  sub-directories of 1Mb or more:
    libs  93.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘buildmer.Rmd’ using rmarkdown
Fitting the final model
Fitting via lmer, with REML: f1 ~ following + vowel + timepoint +
    vowel:timepoint + following:timepoint + (1 + timepoint | word) + (1
    + timepoint + following + timepoint:following | participant)
Finalizing by converting the model to lmerTest
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'buildmer.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘buildmer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bayesian_changepoint_groove_detection.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Bayesian_changepoint_groove_detection.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Bayesian_changepoint_groove_detection.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘bunching_examples.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bunching_examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bunching_examples.Rmd’

--- re-building ‘bunching_theory.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bunching_theory.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bunching_theory.Rmd’

SUMMARY: processing the following files failed:
  ‘bunching_examples.Rmd’ ‘bunching_theory.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘bunching_with_bunchr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bunching_with_bunchr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bunching_with_bunchr.Rmd’

--- re-building ‘notch_estimation.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'notch_estimation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘notch_estimation.Rmd’

SUMMARY: processing the following files failed:
  ‘bunching_with_bunchr.Rmd’ ‘notch_estimation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_plotting.Rmd’ using rmarkdown
Warning: Removed 4550 row(s) containing missing values (geom_path).
Warning in st_point_on_surface.sfc(sf::st_zm(x)) :
  st_point_on_surface may not give correct results for longitude/latitude data
Warning: Removed 3 rows containing missing values (geom_text).
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'simple_plotting.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘simple_plotting.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘examples.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'c3'

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

    %>%

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

    grid, legend

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Adapting_Algorithm_for_CAISEr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Adapting_Algorithm_for_CAISEr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Adapting_Algorithm_for_CAISEr.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘Tutorial.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CAMS_solar_data.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'CAMS_solar_data.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CAMS_solar_data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Making_maps_with_cancensus.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Making_maps_with_cancensus.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Making_maps_with_cancensus.Rmd’

--- re-building ‘cancensus.Rmd’ using rmarkdown
Census data is currently stored temporarily.

 In order to speed up performance, reduce API quota usage, and reduce unnecessary network calls, please set up a persistent cache directory by setting options(cancensus.cache_path = '<path to cancensus cache directory>')

 You may add this option, together with your API key, to your .Rprofile.

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

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cancensus.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cancensus.Rmd’

SUMMARY: processing the following files failed:
  ‘Making_maps_with_cancensus.Rmd’ ‘cancensus.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cansim.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cansim.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cansim.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.2Mb
Error(s) in re-building vignettes:
--- re-building ‘additional_examples.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'additional_examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘additional_examples.Rmd’

--- re-building ‘getting_started.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘getting_started.Rmd’

SUMMARY: processing the following files failed:
  ‘additional_examples.Rmd’ ‘getting_started.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘tests_and_coverage.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'tests_and_coverage.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘tests_and_coverage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘caret.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'caret.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘caret.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘carpenter.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'carpenter.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘carpenter.Rmd’

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

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

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
converting counts to integer mode
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
>   
> data.mageck = stat.mageck(untreated.list = list(CONTROL1, CONTROL2),
+ treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+ norm.fun="median", extractpattern=expression("^(.+?)(_.+)"),
+ mageckfolder=NULL, sort.criteria="neg", adjust.method="fdr", filename = "TEST" , fdr.pval = 0.05)
sh: mageck: command not found
Warning in system(mageckstring) : error in running command
Warning in file(file, "rt") :
  cannot open file 'TEST.gene_summary.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: stat.mageck -> load.file -> read.table -> file
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CaRpools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 940-945 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
biomaRt has encountered an unexpected server error.
Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)
--- failed re-building ‘CaRpools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cartograflow.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Fontconfig error: Cannot load default config file
Warning: Use of `x$flowcum` is discouraged. Use `flowcum` instead.
Warning: Use of `x$linkcum` is discouraged. Use `linkcum` instead.
Warning: Use of `x$flowcum` is discouraged. Use `flowcum` instead.
Warning: Use of `x$flowcum` is discouraged. Use `flowcum` instead.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cartograflow.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cartograflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cartography.Rmd’ using rmarkdown
Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cartography.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cartography.Rmd’

--- re-building ‘cheatsheet.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cheatsheet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cheatsheet.Rmd’

SUMMARY: processing the following files failed:
  ‘cartography.Rmd’ ‘cheatsheet.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cartools.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cartools.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cartools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘fs’ ‘janitor’ ‘tibble’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-usage.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- 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 ‘persistent_player_profiles.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'persistent_player_profiles.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘persistent_player_profiles.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  ../inst/include/SignificantIntervalSearchFais.h:97:17: warning: 'saveSignificantInterval' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ../inst/include/SignificantIntervalSearchFais.h:100:17: warning: 'saveTestableInterval' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/CASMAP.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning: Removed 204 rows containing missing values (geom_point).
Warning: Removed 204 rows containing missing values (geom_point).
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
Error(s) in re-building vignettes:
--- re-building ‘fit_cat.Rmd’ using rmarkdown

Attaching package: 'catenary'

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

    show

── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.3.0     ✔ purrr   0.3.3
✔ tibble  2.1.3     ✔ dplyr   0.8.5
✔ tidyr   1.0.2     ✔ stringr 1.4.0
✔ readr   1.3.1     ✔ forcats 0.5.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Warning: `data_frame()` is deprecated, use `tibble()`.
This warning is displayed once per session.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'fit_cat.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘fit_cat.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Error(s) in re-building vignettes:
--- re-building ‘CausalImpact.Rmd’ using rmarkdown
Loading required package: bsts
Loading required package: BoomSpikeSlab
Loading required package: Boom
Loading required package: MASS

Attaching package: 'Boom'

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

    rWishart


Attaching package: 'BoomSpikeSlab'

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

    knots

Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: xts

Attaching package: 'bsts'

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

    SuggestBurn

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'CausalImpact.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CausalImpact.Rmd’

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

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

> ### Name: loadData
> ### Title: Loads dataset into a DataSet object
> ### Aliases: loadData
> 
> ### ** Examples
> 
> library(rJava)
> mgm_init()
trying URL 'https://cdn.rawgit.com/benoslab/tetradLite/7c16abbd/out/artifacts/tetradLite_jar/tetradLite.jar'
downloaded 9.4 MB

Warning in download.file(url = file_url, mode = "wb", destfile = jarPath) :
  URL 'https://cdn.rawgit.com/benoslab/tetradLite/7c16abbd/out/artifacts/tetradLite_jar/tetradLite.jar': status was 'Transferred a partial file'
Error in download.file(url = file_url, mode = "wb", destfile = jarPath) : 
  download from 'https://cdn.rawgit.com/benoslab/tetradLite/7c16abbd/out/artifacts/tetradLite_jar/tetradLite.jar' failed
Calls: mgm_init -> download.file
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘CausalBoundsMethods.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'CausalBoundsMethods.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CausalBoundsMethods.Rmd’

--- re-building ‘example-code.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'example-code.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘example-code.Rmd’

--- re-building ‘shinyapp.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'shinyapp.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘shinyapp.Rmd’

SUMMARY: processing the following files failed:
  ‘CausalBoundsMethods.Rmd’ ‘example-code.Rmd’ ‘shinyapp.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.4Mb
Error(s) in re-building vignettes:
--- re-building ‘cb2-input-handling.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cb2-input-handling.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cb2-input-handling.Rmd’

--- re-building ‘cb2-tutorial.Rmd’ using rmarkdown
>RAB_3
CTGTAGAAGCTACATCGGCT
>RAB_4
AGCACATACACGAGCGGAAA
>RAB_5
TACCCGTTCAAGTCATCCGC
@BASE1-1
TATTTATTTTGCTACTTAATAATTGGGACTGTGCCCAGCGCGGCGGCAAGAAAAAAATGAAGATTATAATGTGTAATTTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@BASE1-2
TATTTATTTTGCTACTTAATAATTGGGACTCAACTATTGCTGATCATCCTAAAAAAATGAAGATTATAATGTGTAATTTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cb2-tutorial.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cb2-tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘cb2-input-handling.Rmd’ ‘cb2-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Guide-to-CBDA.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Guide-to-CBDA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Guide-to-CBDA.Rmd’

SUMMARY: processing the following file failed:
  ‘Guide-to-CBDA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 119.3Mb
  sub-directories of 1Mb or more:
    libs  118.9Mb
Error(s) in re-building vignettes:
--- re-building ‘CCAMLRGIS.Rmd’ using rmarkdown
Loading required package: sp
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: raster

Attaching package: 'raster'

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

    select



Stratum 2000-1500 may contain up to 31 stations given the distance desired

Stratum 1500-1000 may contain up to 30 stations given the distance desired

Stratum 1000-550 may contain up to 48 stations given the distance desired





Stratum 2000-1500 may contain up to 35 stations given the distance desired

Stratum 1500-1000 may contain up to 28 stations given the distance desired

Stratum 1000-550 may contain up to 51 stations given the distance desired



dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'CCAMLRGIS.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CCAMLRGIS.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
Error(s) in re-building vignettes:
--- re-building ‘ccostr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ccostr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ccostr.Rmd’

--- re-building ‘ccostrSimulation.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ccostrSimulation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ccostrSimulation.Rmd’

SUMMARY: processing the following files failed:
  ‘ccostr.Rmd’ ‘ccostrSimulation.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'quickstart.rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘quickstart.rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cdparcoord.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cdparcoord.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cdparcoord.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   6.2Mb
Package unavailable to check Rd xrefs: ‘rospca’
Error(s) in re-building vignettes:
--- re-building ‘example-masterlist.Rmd’ using rmarkdown

Attaching package: 'censusapi'

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

    getFunction

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'example-masterlist.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘example-masterlist.Rmd’

--- re-building ‘getting-started.Rmd’ using rmarkdown

Attaching package: 'censusapi'

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

    getFunction

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘getting-started.Rmd’

SUMMARY: processing the following files failed:
  ‘example-masterlist.Rmd’ ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘censusr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'censusr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘censusr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘censusxy.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'censusxy.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘censusxy.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ceRtainty.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ceRtainty.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ceRtainty.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GLAD’
Error(s) in re-building vignettes:
--- re-building ‘NEWS.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'NEWS.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘NEWS.Rmd’

--- re-building ‘ChainLadder.Rnw’ using Sweave

Welcome to ChainLadder version 0.2.11

Type vignette('ChainLadder', package='ChainLadder') to access
the overall package documentation.

See demo(package='ChainLadder') for a list of demos.

More information is available on the ChainLadder project web-site:
https://github.com/mages/ChainLadder

To suppress this message use:
suppressPackageStartupMessages(library(ChainLadder))

Loading required package: systemfit
Loading required package: Matrix
Loading required package: car
Loading required package: carData
Loading required package: lmtest
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric


Please cite the 'systemfit' package as:
Arne Henningsen and Jeff D. Hamann (2007). systemfit: A Package for Estimating Systems of Simultaneous Equations in R. Journal of Statistical Software 23(4), 1-40. http://www.jstatsoft.org/v23/i04/.

If you have questions, suggestions, or comments regarding the 'systemfit' package, please use a forum or 'tracker' at systemfit's R-Forge site:
https://r-forge.r-project.org/projects/systemfit/
--- finished re-building ‘ChainLadder.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/changepoint.np.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pbdMPI’
Error(s) in re-building vignettes:
  ...
--- re-building ‘start_checkdown.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'start_checkdown.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘start_checkdown.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cheese.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cheese.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cheese.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘speaq’
Running examples in ‘ChemoSpec-Ex.R’ failed
The error most likely occurred in:

> ### Name: clupaSpectra
> ### Title: Hierarchical Cluster-Based Peak Alignment on a Spectra Object
> ### Aliases: clupaSpectra
> ### Keywords: utilities
> 
> ### ** Examples
> 
> 
> data(alignMUD)
> 
> plotSpectra(alignMUD,
+   which = 1:20, lab.pos = 4.5, offset = 0.1,
+   yrange = c(0, 1900), amp = 500, xlim = c(1.5, 1.8),
+   main = "Misaligned NMR Spectra (alignMUD)"
+ )
> 
> aMUD <- clupaSpectra(alignMUD)
Error in clupaSpectra(alignMUD) : 
  You need to install package speaq to use this function
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘chest-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'chest-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘chest-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'GenomicInteractions', 'Gviz', 'countreg'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Introduction.Rmd’

--- re-building ‘Visualising_Interactions.Rmd’ using rmarkdown
Quitting from lines 41-105 (Visualising_Interactions.Rmd) 
Error: processing vignette 'Visualising_Interactions.Rmd' failed with diagnostics:
there is no package called 'GenomicInteractions'
--- failed re-building ‘Visualising_Interactions.Rmd’

SUMMARY: processing the following files failed:
  ‘Introduction.Rmd’ ‘Visualising_Interactions.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘access_childes_db.Rmd’ using rmarkdown
Using current database version: '2018.1'.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'access_childes_db.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘access_childes_db.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘childhoodmortality.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'childhoodmortality.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘childhoodmortality.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘basic-usage.Rmd’ using rmarkdown
Loading required package: sf
Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "codigo_comuna"
Joining, by = "codigo_comuna"
Warning in st_point_on_surface.sfc(sf::st_zm(x)) :
  st_point_on_surface may not give correct results for longitude/latitude data
Warning in st_point_on_surface.sfc(sf::st_zm(x)) :
  st_point_on_surface may not give correct results for longitude/latitude data
Warning in st_point_on_surface.sfc(sf::st_zm(x)) :
  st_point_on_surface may not give correct results for longitude/latitude data
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- 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 ‘hourly_temperatures.Rmd’ using rmarkdown
Loading required package: chillR
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'hourly_temperatures.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘hourly_temperatures.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cifti_work.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cifti_work.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cifti_work.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘helper_functions.rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'helper_functions.rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘helper_functions.rmd’

--- re-building ‘quickstart.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘quickstart.Rmd’

SUMMARY: processing the following files failed:
  ‘helper_functions.rmd’ ‘quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘CINNA.Rmd’ using rmarkdown

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required namespace: circlize
`geom_smooth()` using formula 'y ~ x'
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'CINNA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CINNA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘CISE_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'CISE_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CISE_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CityWaterBalance_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'CityWaterBalance_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CityWaterBalance_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ckanr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ckanr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ckanr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
Package suggested but not available for checking: ‘rggobi’
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cleanr_Introduction.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cleanr_Introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cleanr_Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown_notangle
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- 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 ‘Overview.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- 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 ‘CliquePercolation.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'CliquePercolation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CliquePercolation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/clpAPI.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ClussCluster.Rmd’ using rmarkdown
s = 2.4
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ClussCluster.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ClussCluster.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘estimate-policyFX.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'estimate-policyFX.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘estimate-policyFX.Rmd’

SUMMARY: processing the following file failed:
  ‘estimate-policyFX.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘clustermole-intro.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'clustermole-intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘clustermole-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Cluster.OBeuOpenCPU.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Cluster.OBeuOpenCPU.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Cluster.OBeuOpenCPU.Rmd’

--- re-building ‘ClusterOBeu.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ClusterOBeu.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ClusterOBeu.Rmd’

SUMMARY: processing the following files failed:
  ‘Cluster.OBeuOpenCPU.Rmd’ ‘ClusterOBeu.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘the_clusterR_package.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘the_clusterR_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Example_on_simulated_data.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Example_on_simulated_data.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Example_on_simulated_data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Package suggested but not available for checking: ‘SingleCellExperiment’
Error(s) in re-building vignettes:
  ...
--- re-building ‘clustree.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'clustree.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘clustree.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘moe430a.db’
Running ‘spelling.R’ [0s/0s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...6c6
< NULL
---
> All Done!
  Running ‘testthat.R’ [22s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("cmsaf")
  Error in R_nc4_create: Permission denied (creation mode was 4096)
  ── 1. Error: (unknown) (@test_extract.level.R#675)  ────────────────────────────
  Error in nc_create!
  Backtrace:
   1. cmsaf::extract.level(...)
   2. cmsaf:::write_output_file(...)
   3. ncdf4::nc_create(outfile, c(vars, grid_vars), force_v4 = force_v4)
  
  149016292920292920149016149016149016149028149016══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 6341 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test_extract.level.R#675) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available:
  'InteractionSet', 'GenomicInteractions',
  'BSgenome.Hsapiens.UCSC.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.5Mb
Package suggested but not available for checking: ‘ridge’
Error(s) in re-building vignettes:
  ...
--- re-building ‘coca-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'coca-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘coca-vignette.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘cocoreg-basics.Rmd’ using rmarkdown
Using  as id variables
Using  as id variables
Using  as id variables
Using  as id variables
Using  as id variables
Using  as id variables
Using  as id variables
Using  as id variables
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cocoreg-basics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cocoreg-basics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘codemeta-intro.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'codemeta-intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘codemeta-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘nih-enrollment-html.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'nih-enrollment-html.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘nih-enrollment-html.Rmd’

SUMMARY: processing the following file failed:
  ‘nih-enrollment-html.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Running-CoDiNA.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 100-105 (Running-CoDiNA.Rmd) 
Error: processing vignette 'Running-CoDiNA.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘Running-CoDiNA.Rmd’

SUMMARY: processing the following file failed:
  ‘Running-CoDiNA.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘adding_cognitoR_to_your_app.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'adding_cognitoR_to_your_app.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘adding_cognitoR_to_your_app.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘coil-vignette.Rmd’ using rmarkdown

Attaching package: 'coil'

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

    frame

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'coil-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘coil-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CollapseLevels.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'CollapseLevels.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CollapseLevels.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  TRA.cpp:235:48: warning: 'drem' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
  TRA.cpp:278:42: warning: 'drem' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
  TRA.cpp:588:51: warning: 'drem' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
  TRA.cpp:673:45: warning: 'drem' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
  TRA.cpp:1006:49: warning: 'drem' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
  TRA.cpp:1233:41: warning: 'drem' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/collapse.Rcheck/00install.out’ for details.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  15.1Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [27s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ── 1. Error: make slides (@test-make_slides.R#23)  ─────────────────────────────
  pandoc document conversion failed with error 6
  Backtrace:
   1. collector::make_slides("Natalie Wade", ques, tmpdir)
   2. rmarkdown::render(...)
   3. rmarkdown:::convert(output_file, run_citeproc)
   4. rmarkdown::pandoc_convert(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 21 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: make slides (@test-make_slides.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘file_structures.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'file_structures.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘file_structures.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘colorBlindness.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'colorBlindness.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘colorBlindness.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘noise.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'noise.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘noise.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Loading required package: colorpatch
Loading required package: ggplot2
Loading required package: grid
Loading required package: gridExtra
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   2.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘colourpicker.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'colourpicker.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘colourpicker.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘colourvision-vignette.Rmd’ using rmarkdown
Fontconfig error: Cannot load default config file
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'colourvision-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘colourvision-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  28.8Mb
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
Packages suggested but not available for checking:
  'inSilicoDb', 'GEOmetadb', 'mogene10sttranscriptcluster.db'
Error(s) in re-building vignettes:
  ...
--- re-building ‘methods-overview.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'methods-overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘methods-overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘formats.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'formats.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘formats.Rmd’

--- re-building ‘manipulation.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'manipulation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘manipulation.Rmd’

SUMMARY: processing the following files failed:
  ‘formats.Rmd’ ‘manipulation.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘completejourney.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'completejourney.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘completejourney.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette_complexity.Rmd’ using rmarkdown
Loading required package: combinat

Attaching package: 'combinat'

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

    combn

Loading required package: shiny
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in base::parse(text = code, keep.source = FALSE) : 
  <text>:21:12: unexpected SPECIAL
20: z2 <- z [ i , 2 ] %InLiNe_IdEnTiFiEr% "#get second restriction value"
21: logical <- %InLiNe_IdEnTiFiEr%
               ^

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'vignette_complexity.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘vignette_complexity.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘comtradr-vignette.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: group_by_() is deprecated. 
Please use group_by() instead

The 'programming' vignette or the tidyeval book can help you
to program with group_by() : https://tidyeval.tidyverse.org
This warning is displayed once per session.
Warning: `as_data_frame()` is deprecated, use `as_tibble()` (but mind the new semantics).
This warning is displayed once per session.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'comtradr-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘comtradr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘examples.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘examples.Rmd’

--- re-building ‘stata.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'stata.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘stata.Rmd’

SUMMARY: processing the following files failed:
  ‘examples.Rmd’ ‘stata.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘condir-examples.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'condir-examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘condir-examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘dbi.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dbi.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dbi.Rmd’

--- re-building ‘no-db.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'no-db.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘no-db.Rmd’

SUMMARY: processing the following files failed:
  ‘dbi.Rmd’ ‘no-db.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Keras.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Keras.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Keras.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction.Rmd’

--- re-building ‘mclust.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'mclust.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘mclust.Rmd’

SUMMARY: processing the following files failed:
  ‘Keras.Rmd’ ‘introduction.Rmd’ ‘mclust.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [66s/96s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(conflicted)
  > 
  > test_check("conflicted")
  ── 1. Failure: shimmed library() returns same as unshimmed (@test-shim.R#50)  ──
  library() not equal to base::library().
  Component "results": 3308 string mismatches
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 30 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: shimmed library() returns same as unshimmed (@test-shim.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘quickdemo.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'quickdemo.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘quickdemo.Rmd’

--- re-building ‘selectionbias.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'selectionbias.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘selectionbias.Rmd’

SUMMARY: processing the following files failed:
  ‘quickdemo.Rmd’ ‘selectionbias.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘chamber.Rmd’ using rmarkdown
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

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'chamber.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘chamber.Rmd’

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

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'senate.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘senate.Rmd’

SUMMARY: processing the following files failed:
  ‘chamber.Rmd’ ‘senate.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 50.9Mb
  sub-directories of 1Mb or more:
    libs  49.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘contrast.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'contrast.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘contrast.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘contribution.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'contribution.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘contribution.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'RODBC', 'MonetDBLite'
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsingCoopGame.Rmd’ using rmarkdown
[WARNING] Could not parse YAML metadata at line 48 column 1: Unexpected '
  '
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'UsingCoopGame.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘UsingCoopGame.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CopulaDTA_Vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'CopulaDTA_Vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CopulaDTA_Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
Running ‘testthat.R’ [6s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 612 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘corpustools.Rmd’ using rmarkdown
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Deleting 1 duplicates
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Deleting 1 duplicates
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'corpustools.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘corpustools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
Package suggested but not available for checking: ‘ProData’
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
Error(s) in re-building vignettes:
--- re-building ‘corrgram_cov2cor.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'corrgram_cov2cor.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘corrgram_cov2cor.Rmd’

--- re-building ‘corrgram_examples.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'corrgram_examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘corrgram_examples.Rmd’

SUMMARY: processing the following files failed:
  ‘corrgram_cov2cor.Rmd’ ‘corrgram_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘databases.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'databases.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘databases.Rmd’

--- re-building ‘using-corrr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'using-corrr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘using-corrr.Rmd’

SUMMARY: processing the following files failed:
  ‘databases.Rmd’ ‘using-corrr.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘corto_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'corto_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘corto_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Introduction.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Introduction.Rmd’

--- re-building ‘bat_WNS.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bat_WNS.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bat_WNS.Rmd’

SUMMARY: processing the following files failed:
  ‘Introduction.Rmd’ ‘bat_WNS.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘countfitteR.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'countfitteR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘countfitteR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘countyflood.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'countyflood.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘countyflood.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘countytimezones.Rmd’ using rmarkdown
Loading required package: acs
Loading required package: stringr
Loading required package: XML

Attaching package: 'acs'

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

    apply


Attaching package: 'dplyr'

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

    combine

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

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

    date

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'countytimezones.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘countytimezones.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘countyweather.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

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

    date

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'countyweather.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘countyweather.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Running ‘testthat.R’ [3s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(covid19us)
  > 
  > test_check("covid19us")
  ── 1. Failure: get_states_daily works (@test-all.R#21)  ────────────────────────
  nrow(too_early) not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 12 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: get_states_daily works (@test-all.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘how_it_works.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'how_it_works.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘how_it_works.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cowbell.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cowbell.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cowbell.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown

********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘coxrt-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'coxrt-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘coxrt-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘coxrt-vignette.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 ‘cpr-pkg.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cpr-pkg.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cpr-pkg.Rmd’

SUMMARY: processing the following file failed:
  ‘cpr-pkg.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cpsurvsim-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cpsurvsim-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cpsurvsim-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(crayon)
  > library(testthat)
  Error: package or namespace load failed for 'testthat' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
   there is no package called 'rlang'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning: code chunks must not depend on the uncached chunk "conditional_mms"
Warning: code chunks must not depend on the uncached chunk "conditional_amces"
Warning: Removed 9 rows containing missing values (position_stack).
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- 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 ‘detect-crop-rows.Rmd’ using rmarkdown
Loading required package: magrittr

Attaching package: 'imager'

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

    add

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

    convolve, spectrum

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

    frame

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

    save.image


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: 'EBImage'

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

    channel, dilate, display, erode, resize, watershed

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'detect-crop-rows.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘detect-crop-rows.Rmd’

SUMMARY: processing the following file failed:
  ‘detect-crop-rows.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘collapse.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'collapse.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘collapse.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'crosswalkr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘crosswalkr.Rmd’

SUMMARY: processing the following files failed:
  ‘collapse.Rmd’ ‘crosswalkr.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘plotting.Rmd’ using rmarkdown

Attaching package: 'crunch'

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

    filter, rstandard, setNames

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

    title

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

    write.csv

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

    table

Loading required package: dplyr

Attaching package: 'dplyr'

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

    combine, filter, id

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'ggplot2'

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

    resolution

Warning in RColorBrewer::brewer.pal(n, pal) :
  n too large, allowed maximum for palette Blues is 9
Returning the palette you asked for with that many colors

Warning: Removed 5 rows containing missing values (geom_point).
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'plotting.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘plotting.Rmd’

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

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

> ### Name: clean_text
> ### Title: Clean text
> ### Aliases: clean_text
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> library(gutenbergr)
> ## let's get Alice's Adventures in Wonderland by Carroll
> # gutenberg_works(author == "Carroll, Lewis") 
> rawText = gutenberg_download(11) ## take the text
Determining mirror for Project Gutenberg from http://www.gutenberg.org/robot/harvest
Error in open.connection(con, "rb") : 
  Recv failure: Connection reset by peer
Calls: gutenberg_download ... datasource_connection -> read_connection -> open -> open.connection
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_crsra.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction_crsra.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction_crsra.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  24.6Mb
Error(s) in re-building vignettes:
--- re-building ‘extending.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'extending.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘extending.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘manual.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'manual.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘manual.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘flexdashboards.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'flexdashboards.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘flexdashboards.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_start_guide.Rmd’ using rmarkdown
trying URL 'http://census.cso.ie/censusasp/saps/boundaries/Census2011_NUTS3_generalised20m.zip'
Content type 'application/x-zip-compressed' length 841102 bytes (821 KB)
==================================================
downloaded 821 KB

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'quick_start_guide.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘quick_start_guide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
Running examples in ‘ctDNAtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: test_ctDNA
> ### Title: Tests the ctDNA positivity of a sample
> ### Aliases: test_ctDNA
> 
> ### ** Examples
> 
> ## Load example data
> data("mutations", package = "ctDNAtools")
> data("targets", package = "ctDNAtools")
> bamT1 <- system.file("extdata", "T1.bam", package = "ctDNAtools")
> bamT2 <- system.file("extdata", "T2.bam", package = "ctDNAtools")
> bamN1 <- system.file("extdata", "N1.bam", package = "ctDNAtools")
> bamN2 <- system.file("extdata", "N2.bam", package = "ctDNAtools")
> bamN3 <- system.file("extdata", "N3.bam", package = "ctDNAtools")
> 
> ## Use human reference genome from BSgenome.Hsapiens.UCSC.hg19 library
> suppressMessages(library(BSgenome.Hsapiens.UCSC.hg19))
Error in library(BSgenome.Hsapiens.UCSC.hg19) : 
  there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Calls: suppressMessages -> withCallingHandlers -> library
Execution halted
Running ‘testthat.R’ [17s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(ctDNAtools)
  > 
  > test_check("ctDNAtools")
  ── 1. Error: (unknown) (@test-ctDNAtest.R#3)  ──────────────────────────────────
  there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
  Backtrace:
   1. base::suppressMessages(library(BSgenome.Hsapiens.UCSC.hg19))
   3. base::library(BSgenome.Hsapiens.UCSC.hg19)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 61 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-ctDNAtest.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ctDNAtools.Rmd’ using rmarkdown
Quitting from lines 42-69 (ctDNAtools.Rmd) 
Error: processing vignette 'ctDNAtools.Rmd' failed with diagnostics:
there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
--- failed re-building ‘ctDNAtools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘akde.Rmd’ using rmarkdown
--- finished re-building ‘akde.Rmd’

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

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

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

Execution halted
SUMMARY: processing the following file failed:
  ‘variogram.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 93.6Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  90.5Mb
Package which this enhances but not available for checking: ‘pbdMPI’
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘page.test.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'page.test.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘page.test.Rmd’

SUMMARY: processing the following file failed:
  ‘page.test.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cumulocityr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cumulocityr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cumulocityr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘customsteps.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: `as.tibble()` is deprecated, use `as_tibble()` (but mind the new semantics).
This warning is displayed once per session.

Attaching package: 'recipes'

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

    step

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'customsteps.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘customsteps.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cqv_versatile.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cqv_versatile.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cqv_versatile.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: MBESS
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cv_versatile.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cv_versatile.Rmd’

SUMMARY: processing the following files failed:
  ‘cqv_versatile.Rmd’ ‘cv_versatile.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cvcrand.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cvcrand.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cvcrand.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘RGtk2’
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_cvms.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction_to_cvms.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Introduction_to_cvms.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   4.7Mb
Error(s) in re-building vignettes:
--- re-building ‘cvxr_intro.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cvxr_intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cvxr_intro.Rmd’

--- re-building ‘version1.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'version1.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘version1.Rmd’

SUMMARY: processing the following files failed:
  ‘cvxr_intro.Rmd’ ‘version1.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
Running ‘testthat.R’ [12s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Types not compatible: character is not integer
  
  Sparseness = 99.09 %
  Sorting covariates by covariateId and rowId
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 245 | SKIPPED: 11 | WARNINGS: 195 | FAILED: 6 ]
  1. Failure: Test basic XY constructor (@test-xyConstructor.R#29) 
  2. Failure: Test basic XY constructor (@test-xyConstructor.R#40) 
  3. Failure: Test basic XY constructor (@test-xyConstructor.R#51) 
  4. Failure: Test COO-constructor (@test-xyConstructor.R#182) 
  5. Failure: Test COO-constructor (@test-xyConstructor.R#191) 
  6. Failure: Test COO-constructor (@test-xyConstructor.R#207) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cytofan_flow_cytometry.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cytofan_flow_cytometry.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cytofan_flow_cytometry.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘autogating_cytometree.Rmd’ using rmarkdown
Loading required package: Rcpp
Loading required package: viridisLite
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'autogating_cytometree.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘autogating_cytometree.Rmd’

--- re-building ‘cytoftree.Rmd’ using rmarkdown
Loading required package: Rcpp
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cytoftree.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cytoftree.Rmd’

SUMMARY: processing the following files failed:
  ‘autogating_cytometree.Rmd’ ‘cytoftree.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cytominer-pipeline.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cytominer-pipeline.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cytominer-pipeline.Rmd’

SUMMARY: processing the following file failed:
  ‘cytominer-pipeline.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘using-dabestr.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'using-dabestr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘using-dabestr.Rmd’

SUMMARY: processing the following file failed:
  ‘using-dabestr.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘pied-flycatchers-1.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'pied-flycatchers-1.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘pied-flycatchers-1.Rmd’

--- re-building ‘pied-flycatchers-2.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'pied-flycatchers-2.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘pied-flycatchers-2.Rmd’

--- re-building ‘weights-1-simulate.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'weights-1-simulate.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘weights-1-simulate.Rmd’

SUMMARY: processing the following files failed:
  ‘pied-flycatchers-1.Rmd’ ‘pied-flycatchers-2.Rmd’
  ‘weights-1-simulate.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘dann.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dann.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dann.Rmd’

--- re-building ‘sub_dann.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'sub_dann.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘sub_dann.Rmd’

SUMMARY: processing the following files failed:
  ‘dann.Rmd’ ‘sub_dann.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_danstat.Rmd’ using rmarkdown
Quitting from lines 95-107 (Introduction_to_danstat.Rmd) 
Error: processing vignette 'Introduction_to_danstat.Rmd' failed with diagnostics:
API did not return text/json
--- failed re-building ‘Introduction_to_danstat.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   3.8Mb
Error(s) in re-building vignettes:
--- re-building ‘DatabionicSwarm.Rmd’ using rmarkdown
Package 'DatabionicSwarm' version 1.1.3.
Type 'citation('DatabionicSwarm')' for citing this R package in publications.

Loading required namespace: parallelDist

     PLEASE NOTE:  The components "delsgs" and "summary" of the
 object returned by deldir() are now DATA FRAMES rather than
 matrices (as they were prior to release 0.0-18).
 See help("deldir").
 
     PLEASE NOTE: The process that deldir() uses for determining
 duplicated points has changed from that used in version
 0.0-9 of this package (and previously). See help("deldir").


dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DatabionicSwarm.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DatabionicSwarm.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘datadigest.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'datadigest.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘datadigest.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘dataexplorer-intro.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dataexplorer-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘datagovsgR-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'datagovsgR-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘datagovsgR-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending_dataMaid.Rmd’ using rmarkdown
Data report generation is finished. Please wait while your output file is being rendered.
Warning: Removed 10 rows containing non-finite values (stat_bin).
Warning: Removed 10 rows containing non-finite values (stat_bin).
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Quitting from lines 730-769 (extending_dataMaid.Rmd) 
Error: processing vignette 'extending_dataMaid.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘extending_dataMaid.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_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 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘get_started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dataMeta_Vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dataMeta_Vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dataMeta_Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘creating_data_packages_in_r.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'creating_data_packages_in_r.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘creating_data_packages_in_r.Rmd’

--- re-building ‘using_data_packages_in_r.Rmd.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'using_data_packages_in_r.Rmd.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘using_data_packages_in_r.Rmd.Rmd’

SUMMARY: processing the following files failed:
  ‘creating_data_packages_in_r.Rmd’ ‘using_data_packages_in_r.Rmd.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [8s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  cars_over_20══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 114 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 16 ]
  1. Error: package can be built from different locations (@test-build-locations.R#19) 
  2. Error: can add a data item (@test-conditional-build.R#19) 
  3. Error: assert_data_version (@test-data-version.R#19) 
  4. Error: data objects are saved incrementally in render_root (@test-datapackager-object-read.R#36) 
  5. Error: data objects can be read from render_root or the data dir (@test-datapackager-object-read.R#54) 
  6. Error: documentation is built via document() (@test-document.R#13) 
  7. Error: package built in different edge cases (@test-edge-cases.R#21) 
  8. Error: manual bump version when data unchanged (@test-manual-version-bump.R#19) 
  9. Error: news file is created (@test-news-update.R#13) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘YAML_CONFIG.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'YAML_CONFIG.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘YAML_CONFIG.Rmd’

--- re-building ‘usingDataPackageR.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Quitting from lines 170-174 (usingDataPackageR.Rmd) 
Error: processing vignette 'usingDataPackageR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘usingDataPackageR.Rmd’

SUMMARY: processing the following files failed:
  ‘YAML_CONFIG.Rmd’ ‘usingDataPackageR.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘datapack-overview.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'datapack-overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘datapack-overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘datapasta-in-the-cloud.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'datapasta-in-the-cloud.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘datapasta-in-the-cloud.Rmd’

--- re-building ‘how-to-datapasta.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'how-to-datapasta.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘how-to-datapasta.Rmd’

SUMMARY: processing the following files failed:
  ‘datapasta-in-the-cloud.Rmd’ ‘how-to-datapasta.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dataRetrieval.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dataRetrieval.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dataRetrieval.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/datasailr.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘DataSpaceR.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DataSpaceR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DataSpaceR.Rmd’

--- re-building ‘Monoconal_Antibody_Data.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Monoconal_Antibody_Data.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Monoconal_Antibody_Data.Rmd’

--- re-building ‘Non_Integrated_Datasets.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Non_Integrated_Datasets.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Non_Integrated_Datasets.Rmd’

SUMMARY: processing the following files failed:
  ‘DataSpaceR.Rmd’ ‘Monoconal_Antibody_Data.Rmd’
  ‘Non_Integrated_Datasets.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 59.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  57.8Mb
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_datasus.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction_to_datasus.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Introduction_to_datasus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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]="webshotcaef3822958a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotcaef3822958a.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
Error(s) in re-building vignettes:
--- re-building ‘DataVisualizations.Rmd’ using rmarkdown
Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required namespace: signal
Loading required namespace: ggExtra
Loading required namespace: DatabionicSwarm
Using statistics for ordering instead of default
Warning: did not converge in 10 iterations
Warning: did not converge in 10 iterations
Warning: did not converge in 10 iterations
Warning: did not converge in 10 iterations
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DataVisualizations.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DataVisualizations.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Introduction.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Introduction.Rmd’

--- re-building ‘performance.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'performance.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘performance.Rmd’

SUMMARY: processing the following files failed:
  ‘Introduction.Rmd’ ‘performance.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘daymetr-vignette.Rmd’ using rmarkdown
Sitename set to default - tmp
Warning in .getCRSfromGridMap4(atts) :
  cannot process these parts of the CRS:
_CoordinateTransformType=Projection
_CoordinateAxisTypes=GeoX GeoY
Warning in daymet_grid_tmean(path = system.file(package = "daymetr", "extdata"),  :
  NAs introduced by coercion
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'daymetr-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘daymetr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘gWidgetsRGtk2’
Error: package ‘RMySQL’ could not be loaded
Execution halted
Error: package ‘RMySQL’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)), 
       call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘verifyWrite.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'verifyWrite.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘verifyWrite.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DBItest.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DBItest.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DBItest.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘dbmss.Rmd’ using rmarkdown
Loading required package: spatstat
Loading required package: spatstat.data
Loading required package: nlme
Loading required package: rpart

spatstat 1.63-3       (nickname: 'Wet paint') 
For an introduction to spatstat, type 'beginner' 


Attaching package: 'spatstat'

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

    marginSums

Loading required package: Rcpp
Loading required package: ggplot2
Warning in wmppp(data.frame(X, Y, PointType)) :
  No column has been found for PointWeight. All point weights have been set to 1.
Warning in wmppp(data.frame(X, Y, PointType)) :
  No window has been specified. A rectangle window containing all points has been used.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dbmss.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dbmss.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Database_Saving.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Database_Saving.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Database_Saving.Rmd’

--- re-building ‘dbparser.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dbparser.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dbparser.Rmd’

SUMMARY: processing the following files failed:
  ‘Database_Saving.Rmd’ ‘dbparser.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  24.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘DealGPL570-introduction.Rmd’ using rmarkdown
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DealGPL570-introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DealGPL570-introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘DealGPL570-introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘debar-algorithm-details.Rmd’ using rmarkdown

Attaching package: 'debar'

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

    frame

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'debar-algorithm-details.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘debar-algorithm-details.Rmd’

--- re-building ‘debar-vignette.Rmd’ using rmarkdown

Attaching package: 'debar'

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

    frame

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'debar-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘debar-vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘debar-algorithm-details.Rmd’ ‘debar-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wildfire_example.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'wildfire_example.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘wildfire_example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘decoder.Rmd’ using rmarkdown
Error: processing vignette 'decoder.Rmd' failed with diagnostics:
there is no package called ‘Rcpp’
--- failed re-building ‘decoder.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘decomposedPSF-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'decomposedPSF-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘decomposedPSF-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘deepdep-comparison.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'deepdep-comparison.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘deepdep-comparison.Rmd’

--- re-building ‘deepdep-package.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'deepdep-package.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘deepdep-package.Rmd’

SUMMARY: processing the following files failed:
  ‘deepdep-comparison.Rmd’ ‘deepdep-package.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ODE_parameter_inference.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ODE_parameter_inference.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ODE_parameter_inference.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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 67.4Mb
  sub-directories of 1Mb or more:
    libs  64.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘demoShiny.Rmd’ using rmarkdown
Warning in readLines(system.file("shiny", "hist.R", package = "demoShiny")) :
  incomplete final line found on '/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/demoShiny.Rcheck/demoShiny/shiny/hist.R'
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'demoShiny.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘demoShiny.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘data_import.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'data_import.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘data_import.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Examples_daily_response.Rmd’ using rmarkdown
Warning: Removed 92 row(s) containing missing values (geom_path).
Warning: Removed 71 row(s) containing missing values (geom_path).
Warning: Removed 124 row(s) containing missing values (geom_path).
Warning: Removed 125 row(s) containing missing values (geom_path).
Warning: Removed 30 row(s) containing missing values (geom_path).
Warning: Removed 8 row(s) containing missing values (geom_path).
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Examples_daily_response.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Examples_daily_response.Rmd’

--- re-building ‘compare_methods_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'compare_methods_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘compare_methods_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘Examples_daily_response.Rmd’ ‘compare_methods_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘denovolyzeR_intro.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'denovolyzeR_intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘denovolyzeR_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘DescriptiveStats.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DescriptiveStats.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DescriptiveStats.Rmd’

--- re-building ‘DescriptiveStatsOPENCPU.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DescriptiveStatsOPENCPU.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DescriptiveStatsOPENCPU.Rmd’

--- re-building ‘DescriptiveStatsObeu.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DescriptiveStatsObeu.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DescriptiveStatsObeu.Rmd’

SUMMARY: processing the following files failed:
  ‘DescriptiveStats.Rmd’ ‘DescriptiveStatsOPENCPU.Rmd’
  ‘DescriptiveStatsObeu.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.5Mb
    libs   3.2Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rsymphony'
Error(s) in re-building vignettes:
  ...
--- re-building ‘design-to-dataframe.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'design-to-dataframe.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘design-to-dataframe.Rmd’

SUMMARY: processing the following file failed:
  ‘design-to-dataframe.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘desplot_examples.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'desplot_examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘desplot_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'dclone', 'dcmle'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘separation.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'separation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘separation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘detzrcr-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'detzrcr-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘detzrcr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dependencies.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dependencies.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dependencies.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘dextergui.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

no column `person_id` provided, automatically generating unique person id's
Fontconfig error: Cannot load default config file
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dextergui.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dextergui.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘multistage_fundamentals.Rmd’ using rmarkdown
Fontconfig error: Cannot load default config file
Computing non-mst profile_tables over an mst design, did you mean to use profile_tables_mst?
Warning: Column `item_id` joining character vector and factor, coercing into character vector
Warning: Removed 33 rows containing missing values (geom_point).
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'multistage_fundamentals.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘multistage_fundamentals.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-dfoliatR.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'intro-to-dfoliatR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘intro-to-dfoliatR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 51.3Mb
  sub-directories of 1Mb or more:
    libs  50.7Mb
Package required but not available: ‘ALL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘DGCA_basic.Rmd’ using rmarkdown

Classifying the differential correlation calls.
Calculating permutation number 1.
Calculating permutation number 2.
Calculating permutation number 3.
Calculating permutation number 4.
Calculating permutation number 5.
Calculating empirical p-values using the permutation sample statistics.
Sorting the combination of the actual and permuted test statistics.
Finding the proportion of each actual test statistic greater than the permuted test statistics.
Calculating qvalues from the empirical p-values.
Classifying the differential correlation calls.
The dotplot_binwidth is 1e-04 and the dotplot_size is 0.913.
Warning: `fun.y` is deprecated. Use `fun` instead.
Warning: `fun.ymin` is deprecated. Use `fun.min` instead.
Warning: `fun.ymax` is deprecated. Use `fun.max` instead.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DGCA_basic.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DGCA_basic.Rmd’

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

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

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  ../inst/include/adept/adept_source.h:560:6: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ../inst/include/adept/adept_source.h:561:6: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ../inst/include/adept/adept_source.h:616:6: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ../inst/include/adept/adept_source.h:617:6: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ../inst/include/adept/adept_source.h:1147:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ../inst/include/adept/adept_source.h:1148:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/dgumbel.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘DHS.rates.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DHS.rates.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DHS.rates.Rmd’

SUMMARY: processing the following file failed:
  ‘DHS.rates.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diagis.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'diagis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘diagis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘dialr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dialr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dialr.Rmd’

--- re-building ‘oneshot.Rmd’ using rmarkdown
Warning: ph_valid() is soft deprecated as of dialr 0.2.0
please use is_valid() instead
Warning: ph_possible() is soft deprecated as of dialr 0.2.0
please use is_possible() instead
Warning: ph_region() is soft deprecated as of dialr 0.2.0
please use get_region() instead
Warning: ph_type() is soft deprecated as of dialr 0.2.0
please use get_type() instead
Warning: ph_format() is soft deprecated as of dialr 0.2.0
please use format.phone() instead
Warning: ph_format() is soft deprecated as of dialr 0.2.0
please use format.phone() instead
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'oneshot.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘oneshot.Rmd’

SUMMARY: processing the following files failed:
  ‘dialr.Rmd’ ‘oneshot.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Basics.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Basics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Basics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘did-basics.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'did-basics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘did-basics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dietr-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dietr-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dietr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diezeit_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'diezeit_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘diezeit_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘diffenrich_vignette.Rmd’ using rmarkdown
Loading required package: kableExtra

Attaching package: 'kableExtra'

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

    group_rows

Scale for 'fill' is already present. Adding another scale for 'fill', which
will replace the existing scale.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'diffenrich_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘diffenrich_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs   1.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.0Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘A_Brief_Example.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'A_Brief_Example.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘A_Brief_Example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘pcaL1’
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘disaggregation.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'disaggregation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘disaggregation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘dissever-demo.Rmd’ using rmarkdown
Loading required package: sp
Loading required package: viridisLite

Attaching package: 'dplyr'

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

    intersect, select, union

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'magrittr'

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

    extract

Loading required package: lattice
Loading required package: ggplot2
Loading required package: gam
Loading required package: splines
Loading required package: foreach
Loaded gam 1.16.1

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dissever-demo.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dissever-demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘prototyping.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'prototyping.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘prototyping.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_disto.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'vignette_disto.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘vignette_disto.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'sendplot', 'HWxtest'
Error(s) in re-building vignettes:
--- re-building ‘getting_started_with_dkanr.Rmd’ using rmarkdown

Attaching package: 'purrr'

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

    is_null


Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

200 records (DKAN nodes) have been retrieved
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'getting_started_with_dkanr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘getting_started_with_dkanr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  16.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘dlstats.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dlstats.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dlstats.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘docstring_intro.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'docstring_intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘docstring_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_document.Rmd’ using rmarkdown
First time using roxygen2. Upgrading automatically...
Updating roxygen version in /private/var/folders/08/nc4f1s3x1jqd9ln5mnvrqzqh0000gp/T/RtmpsBNKFl/document_11dee4adc2032/minimal/DESCRIPTION
Loading minimal
First time using roxygen2. Upgrading automatically...
Updating roxygen version in /private/var/folders/08/nc4f1s3x1jqd9ln5mnvrqzqh0000gp/T/RtmpsBNKFl/document_11deebae1a8/minimal/DESCRIPTION
Loading minimal
First time using roxygen2. Upgrading automatically...
Updating roxygen version in /private/var/folders/08/nc4f1s3x1jqd9ln5mnvrqzqh0000gp/T/RtmpsBNKFl/document_11dee3c9a81e7/simple/DESCRIPTION
Loading simple
First time using roxygen2. Upgrading automatically...
Updating roxygen version in /private/var/folders/08/nc4f1s3x1jqd9ln5mnvrqzqh0000gp/T/RtmpsBNKFl/document_11dee400ca235/minimal/DESCRIPTION
Warning: roxygen2 requires Encoding: UTF-8
Loading minimal
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction_to_document.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Introduction_to_document.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘numbers-in-engineering-format.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'numbers-in-engineering-format.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘numbers-in-engineering-format.Rmd’

--- re-building ‘put-workspace-in-docx.Rmd’ using rmarkdown
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'put-workspace-in-docx.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘put-workspace-in-docx.Rmd’

SUMMARY: processing the following files failed:
  ‘numbers-in-engineering-format.Rmd’ ‘put-workspace-in-docx.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   9.3Mb
Error(s) in re-building vignettes:
--- re-building ‘dodgr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dodgr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dodgr.Rmd’

--- re-building ‘times.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'times.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘times.Rmd’

SUMMARY: processing the following files failed:
  ‘dodgr.Rmd’ ‘times.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Introduction-to-doremi.Rmd’ using rmarkdown
Warning: Model failed to converge with 1 negative eigenvalue: -9.9e-01
Warning in remi(data = mydatab3, id = "id", time = "time", signal = "dampedsignal",  :
  No excitation signal introduced as input. Input was set to 0. Adjustment will consist on exponential fit.

Warning in remi(data = rotation, id = "id", time = "days", signal = "meanRT",  :
  No excitation signal introduced as input. Input was set to 0. Adjustment will consist on exponential fit.

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction-to-doremi.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Introduction-to-doremi.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘doMPI’
Error(s) in re-building vignettes:
--- re-building ‘dotwhisker-vignette.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dotwhisker-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dotwhisker-vignette.Rmd’

--- re-building ‘kl2007_examples.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    combine

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: ggplot2
Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'kl2007_examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘kl2007_examples.Rmd’

SUMMARY: processing the following files failed:
  ‘dotwhisker-vignette.Rmd’ ‘kl2007_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘button_types.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'button_types.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘button_types.Rmd’

--- re-building ‘customization.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'customization.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘customization.Rmd’

--- re-building ‘downloadthis.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'downloadthis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘downloadthis.Rmd’

SUMMARY: processing the following files failed:
  ‘button_types.Rmd’ ‘customization.Rmd’ ‘downloadthis.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dplyrAssist.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dplyrAssist.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dplyrAssist.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
Error(s) in re-building vignettes:
--- re-building ‘dplyr.teradata.Rmd’ using rmarkdown
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: dbplyr

Attaching package: 'dbplyr'

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

    ident, sql

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dplyr.teradata.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dplyr.teradata.Rmd’

SUMMARY: processing the following file failed:
  ‘dplyr.teradata.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘walk_through_in_R.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'walk_through_in_R.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘walk_through_in_R.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘clustermq’
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/DRIP.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘userGuide.Rmd’ using rmarkdown
Fontconfig error: Cannot load default config file
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
Using constraints: b = 1
Using constraints: b = 1
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘userGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ds4psy.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ds4psy.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ds4psy.Rmd’

SUMMARY: processing the following file failed:
  ‘ds4psy.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DSAIDE.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DSAIDE.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DSAIDE.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DSAIRM.Rmd’ using rmarkdown
Loading required package: shiny
Welcome to the DSAIRM package. Type dsairmmenu() to get started.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DSAIRM.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DSAIRM.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dsa-vignette.Rmd’ using rmarkdown
Fontconfig error: Cannot load default config file
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dsa-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dsa-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘start.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'start.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘start.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘dsr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dsr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dsr.Rmd’

--- re-building ‘dsrre.Rmd’ using rmarkdown
Loading required package: frailtypack
Loading required package: survival
Loading required package: boot

Attaching package: 'boot'

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

    aml

Loading required package: MASS
Loading required package: survC1
Loading required package: doBy

Attaching package: 'frailtypack'

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

    cluster

Loading required package: dplyr

Attaching package: 'dplyr'

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

    select

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: dsr
Joining, by = "sex"
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dsrre.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dsrre.Rmd’

SUMMARY: processing the following files failed:
  ‘dsr.Rmd’ ‘dsrre.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dsrTest-example.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dsrTest-example.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dsrTest-example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘translation.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'translation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘translation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DT.Rmd’ using rmarkdown_notangle
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DT.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DT.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.2Mb
Error(s) in re-building vignettes:
--- re-building ‘parallelization-considerations.Rmd’ using rmarkdown_notangle
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'parallelization-considerations.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘parallelization-considerations.Rmd’

--- re-building ‘timing-experiments.Rmd’ using rmarkdown_notangle
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'timing-experiments.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘timing-experiments.Rmd’

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

SUMMARY: processing the following files failed:
  ‘parallelization-considerations.Rmd’ ‘timing-experiments.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘duawranglr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'duawranglr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘duawranglr.Rmd’

--- re-building ‘securing_data.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'securing_data.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘securing_data.Rmd’

SUMMARY: processing the following files failed:
  ‘duawranglr.Rmd’ ‘securing_data.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dvmisc.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dvmisc.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dvmisc.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dynamac-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'dynamac-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘dynamac-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  23.5Mb
Package suggested but not available for checking: ‘destiny’
Running ‘testthat.R’ [19s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ── 2. Error: Perform dimred dm_destiny  ────────────────────────────────────────
  Please install the following packages: 
    "destiny"
  Backtrace:
   1. dyndimred:::method_fun(small_expr)
   2. dynutils::install_packages("destiny")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 191 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 2 ]
  1. Error: Perform dimred dm_destiny 
  2. Error: Perform dimred dm_destiny 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
Loading required package: survival
Loading required package: optimx

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

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TutorialdynRB.Rmd’ using rmarkdown
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-6
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'TutorialdynRB.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘TutorialdynRB.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   3.0Mb
Error(s) in re-building vignettes:
--- re-building ‘linearSDE.Rmd’ using rmarkdown
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LinearSDE.c -o LinearSDE.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o LinearSDE.so LinearSDE.o -L/usr/local/lib -lgsl -lgslcblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'linearSDE.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘linearSDE.Rmd’

--- re-building ‘InstallationForDevelopers.Rnw’ using Sweave
--- finished re-building ‘InstallationForDevelopers.Rnw’

--- re-building ‘InstallationForUsers.Rnw’ using Sweave
--- finished re-building ‘InstallationForUsers.Rnw’

--- re-building ‘LinearDiscreteTimeModels.Rnw’ using Sweave
--- finished re-building ‘LinearDiscreteTimeModels.Rnw’

--- re-building ‘NonlinearContinuousTimeModels.Rnw’ using Sweave
--- finished re-building ‘NonlinearContinuousTimeModels.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘functionality.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'functionality.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘functionality.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs        8.5Mb
    shiny_app   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘eAnalytics.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'eAnalytics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘eAnalytics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   4.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘easypackages-vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'easypackages-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘easypackages-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘easySdcTableVignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'easySdcTableVignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘easySdcTableVignette.Rmd’

--- re-building ‘singletonsAndZeros.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'singletonsAndZeros.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘singletonsAndZeros.Rmd’

SUMMARY: processing the following files failed:
  ‘easySdcTableVignette.Rmd’ ‘singletonsAndZeros.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ecb_sdw.Rmd’ using rmarkdown
Warning: Removed 28 rows containing non-finite values (stat_smooth).
Warning: Removed 28 rows containing missing values (geom_point).
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ecb_sdw.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ecb_sdw.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘eclust.Rmd’ using rmarkdown
See example usage at http://sahirbhatnagar.com/eclust/
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'eclust.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘eclust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘advanced_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'advanced_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘advanced_vignette.Rmd’

--- re-building ‘cds_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'cds_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘cds_vignette.Rmd’

--- re-building ‘webapi_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'webapi_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘webapi_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘advanced_vignette.Rmd’ ‘cds_vignette.Rmd’ ‘webapi_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Barro_Colorado.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Barro_Colorado.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Barro_Colorado.Rmd’

--- re-building ‘coalesc_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'coalesc_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘coalesc_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘Barro_Colorado.Rmd’ ‘coalesc_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_ecospat_package.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'vignette_ecospat_package.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘vignette_ecospat_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EDA.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'EDA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘EDA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘sf::st_make_valid’ by ‘lwgeom::st_make_valid’ when loading ‘edbuildmapr’
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/edbuildmapr.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘filters.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'filters.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘filters.Rmd’

--- re-building ‘metrics.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'metrics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘metrics.Rmd’

SUMMARY: processing the following files failed:
  ‘filters.Rmd’ ‘metrics.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘editData.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'editData.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘editData.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘briefmanual.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'briefmanual.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘briefmanual.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Loading required package: car
Loading required package: carData
Loading required package: lfactors
lfactors v1.0.4

EdSurvey v2.4.0


Attaching package: 'EdSurvey'

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

    cbind, rbind

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- 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 ‘eechidna-intro.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

trying URL 'https://github.com/ropenscilabs/eechidna/raw/master/extra-data/tpp_pp.rda'
Content type 'application/octet-stream' length 1677810 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://github.com/ropenscilabs/eechidna/raw/master/extra-data/nat_map16.rda'
Content type 'application/octet-stream' length 242124 bytes (236 KB)
==================================================
downloaded 236 KB

trying URL 'https://github.com/ropenscilabs/eechidna/raw/master/extra-data/nat_data16.rda'
Content type 'application/octet-stream' length 6528 bytes
==================================================
downloaded 6528 bytes

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'eechidna-intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘eechidna-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘custom-import-function.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'custom-import-function.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘custom-import-function.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘custom-import-function.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [9s/16s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Failure: moves_calc gets the correct results (@test-calculators.R#210)  ──
  `moves` not equal to `correct_result`.
  Component "sid": Modes: character, numeric
  Component "sid": Attributes: < target is NULL, current is list >
  Component "sid": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 509 | SKIPPED: 0 | WARNINGS: 29 | FAILED: 1 ]
  1. Failure: moves_calc gets the correct results (@test-calculators.R#210) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Loading required package: ggplot2
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘eesim.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

This is dlnm 2.3.9. For details: help(dlnm) and vignette('dlnmOverview').
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
This function may take a minute or two to run, especially if you are
creating lots of replications (`n_reps`).
This function may take a minute or two to run, especially if you are
creating lots of replications (`n_reps`).
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'eesim.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘eesim.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EFDR_documents.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'EFDR_documents.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘EFDR_documents.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘effectR.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'effectR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘effectR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ega.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ega.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ega.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 68.3Mb
  sub-directories of 1Mb or more:
    libs  67.6Mb
Error(s) in re-building vignettes:
--- re-building ‘egor_allbus.Rmd’ using rmarkdown
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: tibble
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'egor_allbus.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘egor_allbus.Rmd’

--- re-building ‘using_egor.Rmd’ using rmarkdown
Fontconfig error: Cannot load default config file
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'using_egor.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘using_egor.Rmd’

SUMMARY: processing the following files failed:
  ‘egor_allbus.Rmd’ ‘using_egor.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘EGRETci.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'EGRETci.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘EGRETci.Rmd’

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

Attaching package: 'EGRET'

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

    stitch

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Enhancements.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Enhancements.Rmd’

SUMMARY: processing the following files failed:
  ‘EGRETci.Rmd’ ‘Enhancements.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘eha.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'eha.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘eha.Rmd’

--- re-building ‘parametric.Rnw’ using Sweave
--- finished re-building ‘parametric.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘eHelp.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'eHelp.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘eHelp.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘BiocStyle’
Error(s) in re-building vignettes:
  ...
--- re-building ‘EHRtemporalVariability.Rmd’ using rmarkdown
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘EHRtemporalVariability.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 45.8Mb
  sub-directories of 1Mb or more:
    libs  44.8Mb
Error(s) in re-building vignettes:
--- re-building ‘EIX.Rmd’ using rmarkdown
   [[ suppressing 19 column names 'satisfaction_level', 'last_evaluation', 'number_project' ... ]]
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'EIX.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘EIX.Rmd’

--- re-building ‘titanic_data.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'titanic_data.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘titanic_data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_start.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'quick_start.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘quick_start.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_elevatr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction_to_elevatr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction_to_elevatr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘EloRating_tutorial.Rmd’ using rmarkdown
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: sna
Loading required package: statnet.common

Attaching package: 'statnet.common'

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

    order

Loading required package: network
network: Classes for Relational Data
Version 1.16.0 created on 2019-11-30.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.

sna: Tools for Social Network Analysis
Version 2.5 created on 2019-12-09.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'EloRating_tutorial.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘EloRating_tutorial.Rmd’

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

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

Packages suggested but not available for checking: 'hgu133plus2.db', 'lumi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsingEmbedSOM.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'UsingEmbedSOM.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘UsingEmbedSOM.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘R2jags’
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  11.8Mb
Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CInp2TS
> ### Title: Function to convert Constant Input to Time Series
> ### Aliases: CInp2TS
> ### Keywords: CInp2TS
> 
> ### ** Examples
> 
> library(EmiStatR)
> library(zoo)

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> data("qs_factor")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> 
> cinp.daily.file <- qs_factor
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘creating-EML.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'creating-EML.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘creating-EML.Rmd’

--- re-building ‘working-with-units.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'working-with-units.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘working-with-units.Rmd’

SUMMARY: processing the following files failed:
  ‘creating-EML.Rmd’ ‘working-with-units.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘emojifont.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'emojifont.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘emojifont.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Error(s) in re-building vignettes:
--- re-building ‘EQL.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'EQL.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘EQL.Rmd’

--- re-building ‘emuDB.Rmd’ using rmarkdown
[WARNING] Could not parse YAML metadata at line 15 column 1: Unexpected '
  '
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'emuDB.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘emuDB.Rmd’

--- re-building ‘emuR_intro.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'emuR_intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘emuR_intro.Rmd’

SUMMARY: processing the following files failed:
  ‘EQL.Rmd’ ‘emuDB.Rmd’ ‘emuR_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘enpls.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'enpls.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘enpls.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘enrichR.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'enrichR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘enrichR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_ensembleR.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Introduction_to_ensembleR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Introduction_to_ensembleR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘entropart.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'entropart.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘entropart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘texture.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'texture.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘texture.Rmd’

--- re-building ‘theme_publish.Rmd’ using rmarkdown
Loading required package: envalysis
Loading required package: ggplot2
Saving 8 x 5 in image
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'theme_publish.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘theme_publish.Rmd’

SUMMARY: processing the following files failed:
  ‘texture.Rmd’ ‘theme_publish.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘epicontacts.Rmd’ using rmarkdown
[WARNING] Note with key '1' defined at line 677 column 1 but not used.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘epicontacts.Rmd’

--- re-building ‘epicontacts_class.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'epicontacts_class.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘epicontacts_class.Rmd’

SUMMARY: processing the following files failed:
  ‘epicontacts.Rmd’ ‘epicontacts_class.Rmd’

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

> ### Name: EpiCurve
> ### Title: Plot an Epidemic Curve
> ### Aliases: EpiCurve
> ### Keywords: ~documentation
> 
> ### ** Examples
> 
> # library(Epicurve)
> date <- seq(as.timeDate("2017-05-10 21:35:22"), as.timeDate("2017-05-12 06:15:12"), by="12 min")
> val <- rep(1, length(date))
> tri <- rep(c("Alive", "Died","Unknown"), length.out=length(date))
> DF <- data.frame(date, val, tri)
> names(DF) <- c("date","value", "tri")
> 
> 
> EpiCurve(DF,
+          date = "date",
+          freq = "value",
+          period = "hour",
+          split = 4,
+          cutvar = "tri",
+          ylabel="Number of cases",
+          xlabel= "From 2017-05-10 21:35:22 To 2017-05-12 06:15:12",
+          title = "Epidemic Curve")
Error: Column `DateFactor` is unknown
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘EpiCurve.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: ISOweek
Loading required package: scales
Quitting from lines 149-156 (EpiCurve.Rmd) 
Error: processing vignette 'EpiCurve.Rmd' failed with diagnostics:
Column `DateFactor` is unknown
--- failed re-building ‘EpiCurve.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘demo.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'demo.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘epiflows-class.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'epiflows-class.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epistasis.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'epistasis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘epistasis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Loading required namespace: outbreaks
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘EpiReport_Vignette.Rmd’ using rmarkdown
Warning: Use of `data[[yvar]]` is discouraged. Use `.data[[yvar]]` instead.
Warning: Use of `data[[xvar]]` is discouraged. Use `.data[[xvar]]` instead.
Warning: Use of `data[[movAverage]]` is discouraged. Use `.data[[movAverage]]` instead.
Warning: Use of `data[[xvar]]` is discouraged. Use `.data[[xvar]]` instead.
Fontconfig error: Cannot load default config file
Warning: Use of `data[[min4years]]` is discouraged. Use `.data[[min4years]]` instead.
Warning: Use of `data[[max4years]]` is discouraged. Use `.data[[max4years]]` instead.
Warning: Use of `data[[xvar]]` is discouraged. Use `.data[[xvar]]` instead.
Warning: Use of `data[[mean4years]]` is discouraged. Use `.data[[mean4years]]` instead.
Warning: Use of `data[[xvar]]` is discouraged. Use `.data[[xvar]]` instead.
Warning: Use of `data[[yvar]]` is discouraged. Use `.data[[yvar]]` instead.
Warning: Use of `data[[xvar]]` is discouraged. Use `.data[[xvar]]` instead.
Warning: Use of `data[[xvar]]` is discouraged. Use `.data[[xvar]]` instead.
Warning: Use of `data[[yvar]]` is discouraged. Use `.data[[yvar]]` instead.
Warning: Use of `data[[group]]` is discouraged. Use `.data[[group]]` instead.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'EpiReport_Vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘EpiReport_Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘episensr.Rmd’ using rmarkdown
Warning: Removed 438 rows containing non-finite values (stat_bin).
Warning: Removed 438 rows containing non-finite values (stat_density).
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 2 rows containing non-finite values (stat_bin).
Warning: Removed 2 rows containing non-finite values (stat_density).
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'episensr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘episensr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pvalueplot.Rmd’ using rmarkdown
Confidence interval type is  95%CI
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'pvalueplot.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘pvalueplot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EpiSignalDetection_Vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'EpiSignalDetection_Vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘EpiSignalDetection_Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘EpiStats.Rmd’ using rmarkdown
Loading required package: epiR
Loading required package: survival
Package epiR 1.0-14 is loaded
Type help(epi.about) for summary information
Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses


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

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'EpiStats.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘EpiStats.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘user_guide.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'user_guide.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘user_guide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epubr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'epubr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘epubr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘eq5d.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'eq5d.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘eq5d.Rmd’

SUMMARY: processing the following file failed:
  ‘eq5d.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘equateMultiple_tutorial.Rmd’ using rmarkdown
Loading required package: MASS
Loading required package: msm
Loading required package: polycor
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'equateMultiple_tutorial.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘equateMultiple_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ergm-equations.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ergm-equations.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ergm-equations.Rmd’

--- re-building ‘extending-ergmito.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'extending-ergmito.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘extending-ergmito.Rmd’

SUMMARY: processing the following files failed:
  ‘ergm-equations.Rmd’ ‘extending-ergmito.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   1.8Mb
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ERSA.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ERSA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ERSA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DoseSelectorInterface.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'DoseSelectorInterface.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘DoseSelectorInterface.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘example-analysis.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Linking to liblwgeom 3.0.0beta1 r16016, GEOS 3.7.2, PROJ 5.2.0
Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0

Attaching package: 'sf'

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

    st_make_valid

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'example-analysis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘example-analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘get-started.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'get-started.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘get-started.Rmd’

--- re-building ‘shiny-usage.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'shiny-usage.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘shiny-usage.Rmd’

SUMMARY: processing the following files failed:
  ‘get-started.Rmd’ ‘shiny-usage.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_ess.Rmd’ using rmarkdown

Please cite as: 

Cimentada, Jorge (2019). Download Data from the European Social Survey on the Fly R package version 1.0.2.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'intro_ess.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘intro_ess.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ESTER.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ESTER.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ESTER.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Package required but not available: ‘PSCBS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ethnobotanyr_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ethnobotanyr_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ethnobotanyr_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘extending_etl.Rmd’ using rmarkdown
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

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'extending_etl.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘extending_etl.Rmd’

--- re-building ‘using_etl.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'using_etl.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘using_etl.Rmd’

SUMMARY: processing the following files failed:
  ‘extending_etl.Rmd’ ‘using_etl.Rmd’

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘RODBC’
Running ‘test.etmCIF.R’ [2s/2s]
Running the tests in ‘tests/test.etmCIF.R’ failed.
Last 13 lines of output:
  +     all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P)
  +     all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P)
  + 
  +     scif.control <- summary(cif.control, ci.fun = "cloglog")
  +     scif.exposed <- summary(cif.exposed, ci.fun = "cloglog")
  + 
  +     all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower)
  +     all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper)
  + 
  +     all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower)
  +     all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper)
  + }
  Error in object$n.risk[, trs.sep[i, 1]] : subscript out of bounds
  Calls: summary ... summary -> summary.etm -> ci.transfo -> lapply -> FUN
  Execution halted
Errors in running code in vignettes:
when running code in ‘etmCIF_tutorial.Rnw’
  ...
Call: etmCIF(formula = Surv(entry, exit, cause != 0) ~ group, data = abortion, 
    etype = cause, failcode = 3)

Covariate:  group 
	levels:  0 1 


  When sourcing ‘etmCIF_tutorial.R’:
Error: subscript out of bounds
Execution halted

  ‘etmCIF_tutorial.Rnw’... failed
Error(s) in re-building vignettes:
  ...
--- re-building ‘eudract.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'eudract.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘eudract.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.2Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [25s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9. rmarkdown:::copy_render_intermediates(...)
   10. rmarkdown::find_external_resources(original_input)
   11. rmarkdown:::discover_rmd_resources(input_file, discover_single_resource)
   12. rmarkdown::render(...)
   13. rmarkdown:::convert(output_file, run_citeproc)
   14. rmarkdown::pandoc_convert(...)
  
  # Scenario model: openfair_tef_tc_diff_lm
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 136 | SKIPPED: 4 | WARNINGS: 20 | FAILED: 2 ]
  1. Error: Analyze report renders (@test-reports.R#33) 
  2. Error: Risk Dashboard renders (@test-reports.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘customization.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'customization.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘customization.Rmd’

--- re-building ‘process.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'process.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘process.Rmd’

--- re-building ‘usage.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'usage.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘usage.Rmd’

SUMMARY: processing the following files failed:
  ‘customization.Rmd’ ‘process.Rmd’ ‘usage.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsingEvolutionaryGames.Rmd’ using rmarkdown
[WARNING] Could not parse YAML metadata at line 31 column 1: Unexpected '
  '
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'UsingEvolutionaryGames.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘UsingEvolutionaryGames.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    libs  22.9Mb
Error(s) in re-building vignettes:
--- re-building ‘one-file-at-a-time.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'one-file-at-a-time.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘one-file-at-a-time.Rmd’

--- re-building ‘one-function-at-a-time.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'one-function-at-a-time.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘one-function-at-a-time.Rmd’

--- re-building ‘whole-package.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'whole-package.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘whole-package.Rmd’

SUMMARY: processing the following files failed:
  ‘one-file-at-a-time.Rmd’ ‘one-function-at-a-time.Rmd’
  ‘whole-package.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    exiftool  13.1Mb
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.
Package required but not available: ‘gage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘practical.Rmd’ using rmarkdown
Loading required package: grid
Loading required package: conf.design

Attaching package: 'DoE.base'

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

    aov, lm

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

    plot.design

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

    lengths

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'practical.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘practical.Rmd’

--- re-building ‘include_theory.Rnw’ using Sweave
--- finished re-building ‘include_theory.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘exploreR.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'exploreR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘exploreR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction_en.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction_en.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction_en.Rmd’

--- re-building ‘introduction_fr.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'introduction_fr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction_fr.Rmd’

SUMMARY: processing the following files failed:
  ‘introduction_en.Rmd’ ‘introduction_fr.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_genExPrior.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'using_genExPrior.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘using_genExPrior.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘creating_exposures.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'creating_exposures.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘creating_exposures.Rmd’

--- re-building ‘premium_pattern.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'premium_pattern.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘premium_pattern.Rmd’

--- re-building ‘rate_calculations.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'rate_calculations.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘rate_calculations.Rmd’

SUMMARY: processing the following files failed:
  ‘creating_exposures.Rmd’ ‘premium_pattern.Rmd’
  ‘rate_calculations.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘extremeStat.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'extremeStat.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘extremeStat.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘basics.Rmd’ using rmarkdown
Loading required package: eyelinker
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

Attaching package: 'intervals'

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

    expand

Loading required package: stringr
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'basics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘basics.Rmd’

--- re-building ‘format.Rmd’ using rmarkdown
Loading required package: eyelinker
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'format.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘format.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ezcox.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ezcox.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ezcox.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘getting_started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ezpickr_vignette.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'ezpickr_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ezpickr_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘basics.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'basics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘basics.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘fable.Rmd’ using rmarkdown
Loading required package: fabletools

Attaching package: 'dplyr'

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

    id

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'fable.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘fable.Rmd’

--- re-building ‘transformations.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'transformations.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘transformations.Rmd’

SUMMARY: processing the following files failed:
  ‘fable.Rmd’ ‘transformations.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘fairness.Rmd’ using rmarkdown
Setting direction: controls < cases
Setting direction: controls < cases
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'fairness.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘fairness.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘runit.R’ [36s/99s]
Running the tests in ‘tests/runit.R’ failed.
Last 13 lines of output:
  test_touch: (1 checks) ... OK (2.01 seconds)
  --------------------------- 
  Test file: /Volumes/Builds/packages/high-sierra-x86_64/results/4.0/fakemake.Rcheck/fakemake/runit_tests/runit-throw.R 
  test_exception: (1 checks) ... OK (0 seconds)
  --------------------------- 
  Test file: /Volumes/Builds/packages/high-sierra-x86_64/results/4.0/fakemake.Rcheck/fakemake/runit_tests/runit-xmake.R 
  test_make_full_tree: (4 checks) ... OK (0.05 seconds)
  test_make_missing: (2 checks) ... OK (0.01 seconds)
  test_make_newer: (2 checks) ... OK (1.03 seconds)
  test_make_phony: (3 checks) ... OK (2.04 seconds)
  test_make_prerequisite: (3 checks) ... OK (1.03 seconds)
  test_make_sink: (2 checks) ... OK (0.01 seconds)
  test_make_source_files: (0 checks) ... OK (0 seconds)
  Error: RUnit failed.
  Execution halted
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  16.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.7Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Errata2e.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Errata2e.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Errata2e.Rmd’

SUMMARY: processing the following file failed:
  ‘Errata2e.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      7.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘FateID.Rmd’ using rmarkdown
Quitting from lines 141-142 (FateID.Rmd) 
Error: processing vignette 'FateID.Rmd' failed with diagnostics:
there is no package called 'destiny'
--- failed re-building ‘FateID.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignettes.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'vignettes.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘vignettes.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 39.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  36.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘fdapaceVig.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'fdapaceVig.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘fdapaceVig.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.2Mb
Error(s) in re-building vignettes:
--- re-building ‘feasts.Rmd’ using rmarkdown
Loading required package: fabletools

Attaching package: 'dplyr'

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

    id

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'feasts.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘feasts.Rmd’

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

Error: Vignette re-building failed.
Execution halted