'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.3Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   2.3Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    1.8Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs           22.1Mb
    test_data       2.2Mb
    vignette_data   1.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Error(s) in re-building vignettes:
--- re-building 'intro.rmd' using rmarkdown
trying URL 'https://web.stanford.edu/~hastie/glmnet/glmnetData/Leukemia.RData'
Quitting from lines 167-173 (intro.rmd) 
Error: processing vignette 'intro.rmd' failed with diagnostics:
cannot open URL 'https://web.stanford.edu/~hastie/glmnet/glmnetData/Leukemia.RData'
--- failed re-building 'intro.rmd'

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

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cplexAPI'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
3                  description_url  FALSE
4           description_bugreports  FALSE
5          lintr_assignment_linter   TRUE
6         lintr_line_length_linter   TRUE
7  lintr_trailing_semicolon_linter  FALSE
8       lintr_attach_detach_linter   TRUE
9               lintr_setwd_linter   TRUE
10             lintr_sapply_linter   TRUE
11    lintr_library_require_linter   TRUE
12                lintr_seq_linter   TRUE
13    no_import_package_as_a_whole  FALSE
14               no_export_pattern   TRUE
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  2.09 0.18 2.26 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R   6.5Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'getting-started.Rmd' using rmarkdown
Quitting from lines 27-34 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
File not found; If you want to access non-local files directly, please install the RCurl package!
--- failed re-building 'getting-started.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'printCrudeAndAdjustedModel.Rmd' using rmarkdown
Loading required package: forestplot
Loading required package: grid
Loading required package: checkmate
Loading required package: abind
Loading required package: Gmisc
Loading required package: Rcpp
Loading required package: htmlTable
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

Quitting from lines 70-77 (printCrudeAndAdjustedModel.Rmd) 
Error: processing vignette 'printCrudeAndAdjustedModel.Rmd' failed with diagnostics:
could not find function "%>%"
--- failed re-building 'printCrudeAndAdjustedModel.Rmd'

--- re-building 'timeSplitter.Rmd' using rmarkdown
Loading required package: forestplot
Loading required package: grid
Loading required package: checkmate
Loading required package: abind
Loading required package: Gmisc
Loading required package: Rcpp
Loading required package: htmlTable

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning in coxph(formula = Surv(Start_time, Stop_time, status == "Died from melanoma") ~  :
  a variable appears on both the left and right sides of the formula
Warning in coxph(formula = Surv(Start_time, Stop_time, status == "Died from melanoma") ~  :
  a variable appears on both the left and right sides of the formula
--- finished re-building 'timeSplitter.Rmd'

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

Error: Vignette re-building failed.
Execution halted
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
Package suggested but not available for checking: 'doMC'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    2.6Mb
    libs   2.0Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.5Mb
    libs      2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 182.2Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    java  179.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/h3jsr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs    2.0Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    HaDeX   3.9Mb
    doc     4.0Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  harmony.cpp:211:80: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
See 'd:/Rcompile/CRANpkg/local/4.1/harmony.Rcheck/00install.out' for details.
Running examples in 'harmony-Ex.R' failed
The error most likely occurred in:

> ### Name: HarmonyMatrix
> ### Title: Main Harmony interface
> ### Aliases: HarmonyMatrix
> 
> ### ** Examples
> 
> 
> 
> ## By default, Harmony inputs a normalized gene expression matrix
> ## Not run: 
> ##D harmony_embeddings <- HarmonyMatrix(exprs_matrix, meta_data, 'dataset')
> ## End(Not run)
> 
> ## Harmony can also take a PCA embeddings matrix
> data(cell_lines_small)
> pca_matrix <- cell_lines_small$scaled_pcs
> meta_data <- cell_lines_small$meta_data
> harmony_embeddings <- HarmonyMatrix(pca_matrix, meta_data, 'dataset', 
+                                     do_pca=FALSE)
Harmony 1/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Error in harmonyObj$cluster_cpp() : 
  element-wise pow(): incompatible matrix dimensions: 10x3 and 3x1
Calls: HarmonyMatrix -> harmonize -> cluster -> <Anonymous> -> .External
Execution halted
Running examples in 'harmony-Ex.R' failed
The error most likely occurred in:

> ### Name: HarmonyMatrix
> ### Title: Main Harmony interface
> ### Aliases: HarmonyMatrix
> 
> ### ** Examples
> 
> 
> 
> ## By default, Harmony inputs a normalized gene expression matrix
> ## Not run: 
> ##D harmony_embeddings <- HarmonyMatrix(exprs_matrix, meta_data, 'dataset')
> ## End(Not run)
> 
> ## Harmony can also take a PCA embeddings matrix
> data(cell_lines_small)
> pca_matrix <- cell_lines_small$scaled_pcs
> meta_data <- cell_lines_small$meta_data
> harmony_embeddings <- HarmonyMatrix(pca_matrix, meta_data, 'dataset', 
+                                     do_pca=FALSE)
Harmony 1/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Error in harmonyObj$cluster_cpp() : 
  element-wise pow(): incompatible matrix dimensions: 10x3 and 3x1
Calls: HarmonyMatrix -> harmonize -> cluster -> <Anonymous> -> .External
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(harmony)
  Loading required package: Rcpp
  > 
  > test_check("harmony")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
  
  == Skipped tests ===============================================================
  * Seurat V3 not available (1)
  
  == Failed tests ================================================================
  -- Error (test_integration.R:5:1): (code run outside of `test_that()`) ---------
  <std::logic_error/C++Error/error/condition>
  Error in `harmonyObj$cluster_cpp()`: element-wise pow(): incompatible matrix dimensions: 50x3 and 3x1
  Backtrace:
      x
   1. \-harmony::HarmonyMatrix(...) at test_integration.R:5:0
   2.   \-harmony:::harmonize(harmonyObj, max.iter.harmony, verbose)
   3.     \-harmony:::cluster(harmonyObj)
   4.       \-harmonyObj$cluster_cpp()
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
  Error: Test failures
  Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(harmony)
  Loading required package: Rcpp
  > 
  > test_check("harmony")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
  
  == Skipped tests ===============================================================
  * Seurat V3 not available (1)
  
  == Failed tests ================================================================
  -- Error (test_integration.R:5:1): (code run outside of `test_that()`) ---------
  <std::logic_error/C++Error/error/condition>
  Error in `harmonyObj$cluster_cpp()`: element-wise pow(): incompatible matrix dimensions: 50x3 and 3x1
  Backtrace:
      x
   1. \-harmony::HarmonyMatrix(...) at test_integration.R:5:0
   2.   \-harmony:::harmonize(harmonyObj, max.iter.harmony, verbose)
   3.     \-harmony:::cluster(harmonyObj)
   4.       \-harmonyObj$cluster_cpp()
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'quickstart.Rmd' using rmarkdown
Quitting from lines 148-152 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
element-wise pow(): incompatible matrix dimensions: 79x3 and 3x1
--- failed re-building 'quickstart.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hazer)
  > 
  > test_check("hazer")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  
  == Failed tests ================================================================
  -- Failure (testall.R:22:3): test the haze -------------------------------------
  floor(h$haze * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 225, 224).
  1/1 mismatches
  [1] 224 - 225 == -1
  -- Failure (testall.R:23:3): test the haze -------------------------------------
  floor(h$A0 * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 710, 712).
  1/1 mismatches
  [1] 712 - 710 == 2
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'hedgehog.Rmd' using rmarkdown
Loading required package: testthat
Error: processing vignette 'hedgehog.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'hedgehog.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
    libs      3.9Mb
':::' call which should be '::': 'ggplot2:::guide_axis'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'ggplot2:::build_guides' 'ggplot2:::scales_list'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/highs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'FGN'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   2.3Mb
    libs   2.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
Error(s) in re-building vignettes:
--- re-building 'hockey-ref-scrapers.Rmd' using rmarkdown
Quitting from lines 35-38 (hockey-ref-scrapers.Rmd) 
Error: processing vignette 'hockey-ref-scrapers.Rmd' failed with diagnostics:
no applicable method for 'xml_find_first' applied to an object of class "NULL"
--- failed re-building 'hockey-ref-scrapers.Rmd'

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

SUMMARY: processing the following file failed:
  'hockey-ref-scrapers.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'ROI.plugin.mosek'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.5Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
Running examples in 'htm2txt-Ex.R' failed
The error most likely occurred in:

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

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

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

  mcglm version 0.7.0 (build on 2021-07-07) is now loaded.
----------------------------------------------------------------------
> library(Matrix)
> library(htmcglm)
> 
> data("soya", package = "mcglm")
> 
> form.grain <- grain ~ water * pot
> form.seed <- seeds ~ water * pot
> 
> soya$viablepeasP <- soya$viablepeas / soya$totalpeas
> form.peas <- viablepeasP ~ water * pot
> 
> Z0 <- mc_id(soya)
> Z1 <- mc_mixed(~0 + factor(block), data = soya)
> 
> fit_joint <- mcglm(linear_pred = c(form.grain,
+                                    form.seed,
+                                    form.peas),
+                    matrix_pred = list(c(Z0, Z1),
+                                       c(Z0, Z1),
+                                       c(Z0, Z1)),
+                    link = c("identity",
+                             "log",
+                             "logit"),
+                    variance = c("constant",
+                                 "tweedie",
+                                 "binomialP"),
+                    Ntrial = list(NULL,
+                                  NULL,
+                                  soya$totalpeas),
+                    power_fixed = c(TRUE,TRUE,TRUE),
+                    data = soya)
Automatic initial values selected. 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'forceSymmetric' for signature '"dgCMatrix", "logical"'
Error: $ operator is invalid for atomic vectors
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
GNU make is a SystemRequirements.
Running 'spelling.R' [0s]
  Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hubeau)
  > 
  > test_check("hubeau")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 1 ]
  
  == Skipped tests ===============================================================
  * On CRAN (2)
  
  == Failed tests ================================================================
  -- Error (test-doApiQuery.R:2:3): A query of more than 20000 records -----------
  Error in `curl::curl_fetch_memory(url, handle = handle)`: OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to hubeau.eaufrance.fr:443 
  Backtrace:
       x
    1. +-testthat::expect_error(...) at test-doApiQuery.R:2:2
    2. | \-testthat:::expect_condition_matching(...)
    3. |   \-testthat:::quasi_capture(...)
    4. |     +-testthat (local) .capture(...)
    5. |     | \-base::withCallingHandlers(...)
    6. |     \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. \-hubeau::doApiQuery("indicateurs_services", "communes", params = list())
    8.   \-httr::GET(query, user_agent)
    9.     \-httr:::request_perform(req, hu$handle$handle)
   10.       +-httr:::request_fetch(req$output, req$url, handle)
   11.       \-httr:::request_fetch.write_memory(req$output, req$url, handle)
   12.         \-curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 1 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'design-principles.Rmd' using rmarkdown
--- finished re-building 'design-principles.Rmd'

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'huxtable'

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

    add_rownames

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

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    exdata   6.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(IDConverter)
  > 
  > test_check("IDConverter")
  trying URL 'https://zenodo.org/record/6342397/files/icgc.rda'
  trying URL 'https://zenodo.org/record/6342397/files/pcawg_full.rda'
  trying URL 'https://zenodo.org/record/6342397/files/pcawg_full.rda'
  trying URL 'https://zenodo.org/record/6342397/files/pcawg_full.rda'
  trying URL 'https://zenodo.org/record/6342397/files/pcawg_full.rda'
  trying URL 'https://zenodo.org/record/6342397/files/icgc.rda'
  trying URL 'https://zenodo.org/record/6342397/files/tcga.rda'
  trying URL 'https://zenodo.org/record/6342397/files/pcawg_full.rda'
  [ FAIL 4 | WARN 32 | SKIP 0 | PASS 4 ]
  
  == Failed tests ================================================================
  -- Failure (test-roxytest-testexamples-convert_icgc.R:13:3): Function convert_icgc() @ L25 --
  `convert_pcawg("SA170678")` did not throw an error.
  -- Failure (test-roxytest-testexamples-convert_pcawg.R:19:3): Function convert_pcawg() @ L38 --
  `convert_pcawg("SA5213")` did not throw an error.
  -- Failure (test-roxytest-testexamples-convert_pcawg.R:21:3): Function convert_pcawg() @ L38 --
  `convert_icgc("SP1677", from = "icgc_specimen_id", to = "xx")` did not throw an error.
  -- Failure (test-roxytest-testexamples-convert_tcga.R:13:3): Function convert_tcga() @ L24 --
  `convert_pcawg("TCGA-02-0001-10A-01W-0188-10")` did not throw an error.
  
  [ FAIL 4 | WARN 32 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/IFAA.Rcheck/00install.out' for details.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> model <- univariatePrior("logit-norm", "x1", -1)
> model$priorParam$values[1,1] <- -.6
> model <- mxRun(model)
Running univariatePrior with 1 parameter
> model$output$fit
[1] 0.4515827
> model$output$gradient
x1 
 0 
> model$output$hessian
   x1
x1  8
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  7.55 0.32 7.97 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.2Mb
    libs  13.4Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.7Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    dlib-19.20   8.9Mb
    libs         2.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     16.0Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs   19.3Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.6Mb
    libs   2.0Mb
Running examples in 'immunarch-Ex.R' failed
The error most likely occurred in:

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

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

Processing "<initial>" ...
  -- [1/1] Parsing "D:/temp/RtmpG6GzLI/RLIBS_17cf443145ea3/immunarch/extdata/io/Sample1.tsv.gz" -- immunarch

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

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

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

Done!

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

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

Error in .split_to_batches(.path, "<initial>") : 
  Input file or directory not found: D:/temp/RtmpG6GzLI/RLIBS_17cf443145ea3/immunarch/extdata/io/
Calls: repLoad -> .split_to_batches
Execution halted
Running examples in 'immunarch-Ex.R' failed
The error most likely occurred in:

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

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

Processing "<initial>" ...
  -- [1/1] Parsing "D:/temp/RtmpG6GzLI/RLIBS_17cf443145ea3/immunarch/extdata/io/Sample1.tsv.gz" -- immunarch

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

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

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

Done!

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

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

Error in .split_to_batches(.path, "<initial>") : 
  Input file or directory not found: D:/temp/RtmpG6GzLI/RLIBS_17cf443145ea3/immunarch/extdata/io/
Calls: repLoad -> .split_to_batches
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'accdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.1Mb
    libs   2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
GNU make is a SystemRequirements.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field should be the URL of a single webpage
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc   9.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
File 'iotools/libs/i386/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

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

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

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

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

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

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

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
Running examples in 'IsoMemo-Ex.R' failed
The error most likely occurred in:

> ### Name: getData
> ### Title: API wrapper that fetches data from IsoMemo Applications
> ### Aliases: getData
> 
> ### ** Examples
> 
> getData(db = "IntChron")
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: getData ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(IsoMemo)
  > 
  > test_check("IsoMemo")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  
  == Failed tests ================================================================
  -- Error (test-01-getData.R:2:3): getData() actually retrieves all data --------
  Error in `open.connection(con, "rb")`: cannot open the connection
  Backtrace:
      x
   1. \-IsoMemo::getData() at test-01-getData.R:2:2
   2.   \-IsoMemo::getDatabaseList()
   3.     \-IsoMemo:::callAPI("dbsources")
   4.       \-jsonlite::fromJSON(url)
   5.         \-jsonlite:::parse_and_simplify(...)
   6.           \-jsonlite:::parseJSON(txt, bigint_as_char)
   7.             \-jsonlite:::parse_con(txt, bigint_as_char)
   8.               +-base::open(con, "rb")
   9.               \-base::open.connection(con, "rb")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'Using-IsoMemo-API.Rmd' using rmarkdown
Quitting from lines 21-23 (Using-IsoMemo-API.Rmd) 
Error: processing vignette 'Using-IsoMemo-API.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'Using-IsoMemo-API.Rmd'

SUMMARY: processing the following file failed:
  'Using-IsoMemo-API.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   5.3Mb
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.3Mb
    data   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'locClass'
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           9.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'janitor.Rmd' using rmarkdown

Attaching package: 'janitor'

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

    chisq.test, fisher.test

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: unable to re-encode 'helper_letter.convert.R' lines 353, 354, 356, 499
See 'd:/Rcompile/CRANpkg/local/4.1/JATSdecoder.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'JFE-Ex.R' failed
The error most likely occurred in:

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

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

Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/landsepi.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/leapp.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   8.8Mb
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'less-Ex.R' failed
The error most likely occurred in:

> ### Name: test_timing
> ### Title: Compare Fitting Time
> ### Aliases: test_timing
> 
> ### ** Examples
> 
> X <- matrix(sample(100, 20), nrow = 10)
> y <- sample(100, 10)
> test_timing(1, X, y)
Error in barplot.default(unlist(timings), main = "Fitting Time of Different Regressors",  : 
  log scale error: at least one 'height + offset' value <= 0
Calls: test_timing -> barplot -> barplot.default
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Package unavailable to check Rd xrefs: 'doMC'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    doc       1.0Mb
    extdata   1.1Mb
    libs      3.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   2.1Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Codoc mismatches from documentation object 'gloss_example':
gloss_example
  Code: function(transliteration, glosses, free_translation = "",
                 comment = "", annotation = NULL, grammaticality =
                 NULL, audio_path = NULL, audio_label = "<U+266A>",
                 video_path = NULL, video_width = 320, video_height =
                 240, line_length = 70, italic_transliteration = TRUE,
                 drop_transliteration = FALSE, intext = FALSE,
                 write_to_db = TRUE)
  Docs: function(transliteration, glosses, free_translation = "",
                 comment = "", annotation = NULL, grammaticality =
                 NULL, audio_path = NULL, audio_label = "<U+266A>",
                 video_path = NULL, video_width = 320, video_height =
                 240, line_length = 70, italic_transliteration = TRUE,
                 drop_transliteration = FALSE, intext = FALSE,
                 write_to_db = TRUE)
  Mismatches in argument default values:
    Name: 'audio_label' Code: "<U+266A>" Docs: "<U+266A>"
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.0Mb
    libs       2.7Mb
    testdata   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/container/detail/copy_move_algo.hpp:184:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/container/detail/copy_move_algo.hpp:199:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/container/detail/copy_move_algo.hpp:912:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.1/lolog.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/loon.tourr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/lrstat.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs   2.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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/4.1/lwgeom.Rcheck/00install.out' for details.
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
Found the following significant warnings:
  lxb.c:62:21: warning: '%d' directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.1/lxb.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(madrat)
  Loading required package: magclass
  > 
  > test_check("madrat")
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 386 ]
  
  == Skipped tests ===============================================================
  * On CRAN (6)
  * reshape2 cannot be loaded (1)
  
  == Failed tests ================================================================
  -- Failure (test-config.R:3:3): cache folder can be set properly ---------------
  getwd() not identical to getConfig("cachefolder").
  1/1 mismatches
  x[1]: "d:/Rcompile/CRANpkg/local/4.1/madrat.Rcheck/tests/testthat"
  y[1]: "d:/RCompile/CRANpkg/local/4.1/madrat.Rcheck/tests/testthat"
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 386 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Package suggested but not available for checking: 'doMC'
installed size is  5.2Mb
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installed size is 77.5Mb
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    libs  70.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/magrittr.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    doc    3.5Mb
'LazyData' is specified without a 'data' directory
installed size is 33.5Mb
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installed size is 11.8Mb
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    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs          6.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    doc    2.8Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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    examples   2.7Mb
    libs       2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
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    doc   3.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'flashr'
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installed size is  7.7Mb
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    libs   3.2Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'doMC'
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'cplexAPI'
installed size is  7.1Mb
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Running examples in 'mcglm-Ex.R' failed
The error most likely occurred in:

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

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

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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installed size is  7.4Mb
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    doc   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
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    doc       1.9Mb
    extdata   5.2Mb
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  8.2Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    libs   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    R     1.3Mb
    doc   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    data   2.7Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'genuMet'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
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    doc    2.3Mb
    help   2.0Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
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    R      1.6Mb
    doc    2.4Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    doc   4.6Mb
installed size is  5.0Mb
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    doc    2.2Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'microcontax.data'
Package unavailable to check Rd xrefs: 'microcontax.data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
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    doc    5.2Mb
    lib    1.0Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
Package suggested but not available for checking: 'gurobi'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/MIRES.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'missForest_1.5.Rnw' using Sweave
Loading required package: foreach
Loading required package: missForest
Warning in file(file, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/mixhvg.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 54.5Mb
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    libs  54.1Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
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Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/mlrCPO.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.5Mb
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'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
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    images   1.1Mb
    shiny   14.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
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    doc    1.3Mb
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/mnormt.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'alstructure'

Package which this enhances but not available for checking: 'MoBPSmaps'
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > library(testthat)
  > library(mockthat)
  
  Attaching package: 'mockthat'
  
  The following objects are masked from 'package:testthat':
  
      local_mock, with_mock
  
  > 
  > test_check("mockthat")
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 65 ]
  
  == Failed tests ================================================================
  -- Failure (test-with-mock.R:51:3): can mock in package ------------------------
  `res` not identical to "mocked request".
  Modes: list, character
  names for target but not for current
  Length mismatch: comparison on first 1 components
  Component 1: Modes: list, character
  Component 1: names for target but not for current
  Component 1: Component 1: 1 string mismatch
  -- Failure (test-with-mock.R:60:3): can mock in package ------------------------
  `res` not identical to "mocked request".
  1/1 mismatches
  x[1]: "4"
  y[1]: "mocked request"
  -- Failure (test-with-mock.R:70:3): can create mock from return value ----------
  `res` not identical to "mocked request".
  Modes: list, character
  names for target but not for current
  Length mismatch: comparison on first 1 components
  Component 1: Modes: list, character
  Component 1: names for target but not for current
  Component 1: Component 1: 1 string mismatch
  -- Failure (test-with-mock.R:80:3): can create mock from return value ----------
  `res` not identical to "mocked request".
  Modes: list, character
  names for target but not for current
  Length mismatch: comparison on first 1 components
  Component 1: Modes: list, character
  Component 1: names for target but not for current
  Component 1: Component 1: 1 string mismatch
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 65 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.7Mb
    libs   2.5Mb
installed size is  7.3Mb
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    data   2.1Mb
installed size is 14.7Mb
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    htmlwidgets  14.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
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    data   2.0Mb
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Running 'testthat.R' [32s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(motifr)
  > library(reticulate)
  > 
  > test_check("motifr")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]
  
  == Failed tests ================================================================
  -- Error (test-core.R:43:3): io_undirected_dummy_net_issue#27 ------------------
  <Rcpp::exception/C++Error/error/condition>
  Error in `py_call_impl(callable, dots$args, dots$keywords)`: TypeError: 'float' object cannot be interpreted as an integer
  
  Backtrace:
       x
    1. +-reticulate::py_suppress_warnings(motif_summary(ml_net27, lvl_attr = "lvl")) at test-core.R:43:2
    2. | +-base::with(warnings$catch_warnings(), expr)
    3. | \-reticulate:::with.python.builtin.object(...)
    4. |   +-base::tryCatch(...)
    5. |   | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
    6. |   \-base::force(expr)
    7. \-motifr::motif_summary(ml_net27, lvl_attr = "lvl")
    8.   \-motifr::motifs_distribution(...)
    9.     \-pkg.env$sma$distributionMotifsAutoR(...)
   10.       \-reticulate:::py_call_impl(callable, dots$args, dots$keywords)
  -- Error (test-count_motifs.R:101:3): exemplify_motif --------------------------
  <Rcpp::exception/C++Error/error/condition>
  Error in `py_call_impl(callable, dots$args, dots$keywords)`: StopIteration
  
  Backtrace:
      x
   1. +-testthat::expect_null(...) at test-count_motifs.R:101:2
   2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
   3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
   4. \-motifr::exemplify_motif(motifr::tidygraph_dummy_net, "1,2[I.B]")
   5.   \-pkg.env$sma$exemplifyMotif(py_g, motif)
   6.     \-reticulate:::py_call_impl(callable, dots$args, dots$keywords)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]
  Error: Test failures
  Execution halted
installed size is  5.3Mb
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    data   2.0Mb
    libs   2.5Mb
installed size is  5.7Mb
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    R      1.4Mb
    libs   1.9Mb
Package suggested but not available for checking: 'corpus.useR.2008.abstracts'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/mpmi.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   4.1Mb
    libs   2.4Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'leukemiasEset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  12.7Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/mvdalab.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    1.1Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'asreml'
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     4.8Mb
    models   1.1Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Error(s) in re-building vignettes:
--- re-building 'neighbours.Rnw' using Sweave
Loading required namespace: NMOF
Loading required namespace: quadprog
Warning in par(old.par) : graphical parameter "cin" cannot be set
Warning in par(old.par) : graphical parameter "cra" cannot be set
Warning in par(old.par) : graphical parameter "csi" cannot be set
Warning in par(old.par) : graphical parameter "cxy" cannot be set
Warning in par(old.par) : graphical parameter "din" cannot be set
Warning in par(old.par) : graphical parameter "page" cannot be set
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "neighbours.tex" --max-iterations=20 -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'neighbours.Rnw' failed with diagnostics:
running 'texi2dvi' on 'neighbours.tex' failed

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

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


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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    CppCode   2.8Mb
    R         6.2Mb
    include   5.8Mb
    libs      2.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/nleqslv.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 41-45 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    doc       5.7Mb
    extdata   1.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.0Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'odetector.Rmd' using rmarkdown
Error: processing vignette 'odetector.Rmd' failed with diagnostics:
there is no package called 'prettydoc'
--- failed re-building 'odetector.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'library' or 'require' call not declared from: 'name'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Package suggested but not available for checking: 'cmdstanr'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'unix'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    exampledata   1.5Mb
    libs          2.7Mb
GNU make is a SystemRequirements.
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs   24.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    R        2.6Mb
    libs     8.2Mb
    models   4.7Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Package suggested but not available for checking: 'openNLPmodels.en'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.7Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   1.3Mb
    libs      2.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.8Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.3Mb
Package suggested but not available for checking: 'rrelaxiv'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'package_introduction.Rmd' using rmarkdown
Quitting from lines 204-212 (package_introduction.Rmd) 
Error: processing vignette 'package_introduction.Rmd' failed with diagnostics:
Package `collapse` required for this function to work.
  Please install it by running `install.packages(`collapse`)`.
--- failed re-building 'package_introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    libs   2.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'owidR-Ex.R' failed
The error most likely occurred in:

> ### Name: owid_plot
> ### Title: Plot an owid dataset
> ### Aliases: owid_plot
> ### Keywords: internal
> 
> ### ** Examples
> 
> 
> human_rights <- owid("human-rights-scores")
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: owid ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
Error(s) in re-building vignettes:
--- re-building 'basic-usage.Rmd' using rmarkdown
trying URL 'https://c14.arch.ox.ac.uk/OxCalDistribution.zip'
Content type 'application/zip' length 4396004 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
MCMC analysis
Sort	Burn	Trial	Save	Shrink	kPasses	Done	Ok	Convergence
[.]	[.]	[.]	[.]		3.0	10.0	100.0	100.0
[.]	[.]	[.]	[.]		6.0	20.0	100.0	69.9
[.]	[.]	[.]	[.]		12.0	22.2	100.0	82.6
[.]	[.]	[.]	[.]	[.]	24.0	22.2	100.0	89.4
[.]	[.]	[.]	[.]		48.0	22.2	100.0	94.2
[.]	[.]	[.]	[.]		96.0	22.2	100.0	97.5
[.]	[.]	[.]	[.]		144.0	33.3	100.0	97.5
[.]	[.]	[.]	[.]		192.0	44.4	100.0	97.5
[.]	[.]	[.]	[.]		240.0	55.6	100.0	97.5
[.]	[.]	[.]	[.]		288.0	66.7	100.0	97.5
[.]	[.]	[.]	[.]		336.0	77.8	100.0	97.5
[.]	[.]	[.]	[.]		384.0	88.9	100.0	97.5
[.]	[.]	[.]	[.]		432.0	100.0	100.0	97.5
[.]	[.]	[.]	[.]		480.0	111.1	100.0	97.5
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'basic-usage.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    doc    1.3Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    library  30.0Mb
Package which this enhances but not available for checking: 'CorShrink'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'overview.Rmd' using rmarkdown

Attaching package: 'paleobuddy'

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

    co2

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Checking should be performed on sources prepared by 'R CMD build'.
GNU make is a SystemRequirements.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.5Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.9Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   6.8Mb
NB: this package is only installed for sub-architecture 'x64'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs   13.6Mb
    share  12.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'PeakSegJoint-Ex.R' failed
The error most likely occurred in:

> ### Name: PeakSegJointError
> ### Title: PeakSegJointError
> ### Aliases: PeakSegJointError
> 
> ### ** Examples
> 
> 
> library(PeakSegJoint)
> data(H3K36me3.TDH.other.chunk1, envir=environment())
> lims <- c(43000000, 43200000) # left
> some.counts <-
+   subset(H3K36me3.TDH.other.chunk1$counts,
+          lims[1] < chromEnd & chromStart < lims[2])
> some.regions <-
+   subset(H3K36me3.TDH.other.chunk1$regions,
+          lims[1] < chromEnd & chromStart < lims[2])
> fit <- PeakSegJointSeveral(some.counts)
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > suite <- Sys.getenv("TEST_SUITE")
  > if(suite=="")suite <- NULL
  > test_check("PeakSegJoint", filter=suite)
  Loading required package: PeakSegJoint
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   4.3Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
GNU make is a SystemRequirements.
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:11983 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11983 (sockconn)
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs        2.0Mb
    xvg-files   3.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dendextendRcpp'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Note: possible error in 'simplify2array(msg, except = 0L)': unused argument (except = 0) 
See 'd:/Rcompile/CRANpkg/local/4.1/personalized.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
xgb_cv_personalized: possible error in simplify2array(msg, except =
  0L): unused argument (except = 0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    application   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
    libs      2.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
at_trans : <anonymous>: no visible global function definition for
  'viewportTransform'
at_trans : <anonymous>: no visible global function definition for
  'groupShear'
at_trans : <anonymous>: no visible global function definition for
  'groupFlip'
grobCoords.pp_grobCoords: no visible global function definition for
  'emptyGrobCoords'
grobCoords.pp_ps_transformation: no visible global function definition
  for 'emptyGrobCoords'
makeContent.pp_transformation: no visible global function definition
  for 'defineGrob'
makeContent.pp_transformation: no visible global function definition
  for 'useGrob'
transformationGrob: no visible binding for global variable
  'viewportTransform'
xylists_to_grobcoords: no visible global function definition for
  'emptyGrobCoords'
xylists_to_grobcoords: no visible global function definition for
  'gridCoords'
xylists_to_grobcoords : <anonymous>: no visible global function
  definition for 'gridCoords'
xylists_to_grobcoords: no visible global function definition for
  'gridGrobCoords'
Undefined global functions or variables:
  defineGrob emptyGrobCoords gridCoords gridGrobCoords groupFlip
  groupShear useGrob viewportTransform
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ggsubplot'
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    bin    8.6Mb
    doc    1.2Mb
    libs   1.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'monocle3', 'ProjecTILs', 'SeuratWrappers'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    tests   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pollimetrydata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   2.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.1Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(popsom)
  > 
  > test_check("popsom")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  
  == Failed tests ================================================================
  -- Failure (test-predict.R:12:3): map.predict function works -------------------
  p[56, 1] (`actual`) not equal to "versicolor" (`expected`).
  
  `actual`:   "virginica" 
  `expected`: "versicolor"
  -- Failure (test-predict.R:13:3): map.predict function works -------------------
  p[145, 1] (`actual`) not equal to "virginica" (`expected`).
  
  `actual`:   "versicolor"
  `expected`: "virginica" 
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  Error: Test failures
  Execution halted
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(popsom)
  > 
  > test_check("popsom")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  
  == Failed tests ================================================================
  -- Failure (test-predict.R:12:3): map.predict function works -------------------
  p[56, 1] (`actual`) not equal to "versicolor" (`expected`).
  
  `actual`:   "virginica" 
  `expected`: "versicolor"
  -- Failure (test-predict.R:13:3): map.predict function works -------------------
  p[145, 1] (`actual`) not equal to "virginica" (`expected`).
  
  `actual`:   "versicolor"
  `expected`: "virginica" 
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Loading_and_manipulating.Rmd' using rmarkdown
Error: processing vignette 'Loading_and_manipulating.Rmd' failed with diagnostics:
Using anchor_sections requires Pandoc 2.0+
--- failed re-building 'Loading_and_manipulating.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinyApp   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gurobi', 'Rcplex'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.8Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    4.6Mb
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      2.3Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.3Mb
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rdt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'pspatreg-Ex.R' failed
The error most likely occurred in:

> ### Name: impactsnopar
> ### Title: Compute direct, indirect and total impacts functions for
> ###   continous non-parametric covariates in semiparametric spatial
> ###   regression models.
> ### Aliases: impactsnopar
> 
> ### ** Examples
> 
> ################################################
> # Examples using spatial data of Ames Houses.
> ###############################################
> # Getting and preparing the data
> library(pspatreg)
> library(spdep)
Loading required package: sp
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
Loading required package: sf
Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 7.2.1; sf_use_s2() is TRUE
> library(sf)
> ames <- AmesHousing::make_ames() # Raw Ames Housing Data
> ames_sf <- st_as_sf(ames, coords = c("Longitude", "Latitude"))
> ames_sf$Longitude <- ames$Longitude
> ames_sf$Latitude <- ames$Latitude
> ames_sf$lnSale_Price <- log(ames_sf$Sale_Price)
> ames_sf$lnLot_Area <- log(ames_sf$Lot_Area)
> ames_sf$lnTotal_Bsmt_SF <- log(ames_sf$Total_Bsmt_SF+1)
> ames_sf$lnGr_Liv_Area <- log(ames_sf$Gr_Liv_Area)
> ########### Constructing the spatial weights matrix
> ames_sf1 <- ames_sf[(duplicated(ames_sf$Longitude) == FALSE), ]
> coord_sf1 <- cbind(ames_sf1$Longitude, ames_sf1$Latitude)
> ID <- row.names(as(ames_sf1, "sf"))
> col_tri_nb <- tri2nb(coord_sf1)
> soi_nb <- graph2nb(soi.graph(col_tri_nb, 
+                             coord_sf1), 
+                    row.names = ID)
Error in soi.graph(col_tri_nb, coord_sf1) : dbscan required
Calls: graph2nb -> soi.graph
Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    libs         1.3Mb
    staticdocs   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
NB: this package is only installed for sub-architecture 'x64'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    4.4Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      5.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      2.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   2.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.9Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Error(s) in re-building vignettes:
--- re-building 'textmodel_performance.Rmd' using rmarkdown
Quitting from lines 32-39 (textmodel_performance.Rmd) 
Error: processing vignette 'textmodel_performance.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'textmodel_performance.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/Quartet.Rcheck/00install.out' for details.
Running examples in 'queryup-Ex.R' failed
The error most likely occurred in:

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! pdfTeX error (ext4): \pdfendlink ended up in different nesting level than \pd
fstartlink.
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1 \begin{theindex}
!  ==> Fatal error occurred, no output PDF file produced!
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
'library' or 'require' call to 'RDCOMClient' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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    htmlwidgets   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.6Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
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installed size is 11.6Mb
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    htmlwidgets   6.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
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    R      3.8Mb
    libs   2.0Mb
Running examples in 'rangeBuilder-Ex.R' failed
The error most likely occurred in:

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

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

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

  |                                                  | 0 % ~calculating  Error in sp::spTransform(pts, CRS("+proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +ellps=WGS84 +units=m +no_defs")) : 
  package rgdal is required for spTransform methods
Calls: coordError -> <Anonymous> -> FUN -> <Anonymous> -> <Anonymous>
Execution halted
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
installed size is  8.6Mb
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    data   3.6Mb
    doc    1.5Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   1.0Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ROpenOffice'
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.2Mb
    po    2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
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    corpora   7.4Mb
installed size is  6.6Mb
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installed size is  9.7Mb
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    include   6.6Mb
    libs      2.3Mb
installed size is 44.9Mb
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installed size is  7.3Mb
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    libs   6.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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    lib       4.6Mb
GNU make is a SystemRequirements.
installed size is 11.7Mb
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    doc       1.1Mb
    include   6.4Mb
    libs      2.6Mb
installed size is  9.3Mb
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    jsonexamples   3.8Mb
    libs           3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/rcrypt.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/RCurl.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'R.devices-overview.tex.rsp' using rsp
R.devices v2.17.1 (2022-06-21 08:00:02 UTC) successfully loaded. See ?R.devices for help.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "R.devices-overview.tex" --max-iterations=20 -I "d:/RCompile/CRANpkg/local/4.1/R.devices.Rcheck/vign_test/R.devices/vignettes" -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'R.devices-overview.tex.rsp' failed with diagnostics:
running 'texi2dvi' on 'R.devices-overview.tex' failed

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

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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    data   1.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dataui'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
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    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
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'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/recometrics.Rcheck/00install.out' for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.0Mb
installed size is  5.9Mb
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    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(refund.shiny)
  > 
  > test_check("refund.shiny")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 5 ]
  
  == Skipped tests ===============================================================
  * empty test (1)
  
  == Failed tests ================================================================
  -- Error (test-registration.R:22:3): no errors arise for gaussian registration plots --
  Error in `register_fpca(Y = registration_data, family = "gaussian")`: Please either specify 'npc' or 'npc_criterion' appropriately.
  Backtrace:
      x
   1. \-registr::register_fpca(Y = registration_data, family = "gaussian") at test-registration.R:22:2
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 5 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'ExampleBinary.md' using md
Error: processing vignette 'ExampleBinary.md' failed with diagnostics:
there is no package called 'markdown'
--- failed re-building 'ExampleBinary.md'

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

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

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

Error: Vignette re-building failed.
Execution halted
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

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

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

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

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

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

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

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs      2.5Mb
    swagger   1.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs      3.3Mb
    models    1.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    doc       3.8Mb
    extdata   2.6Mb
    java     26.1Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/Rforestry.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 112.7Mb
  sub-directories of 1Mb or more:
    doc        3.7Mb
    gdal       2.2Mb
    libs      94.3Mb
    pictures   1.3Mb
    proj       8.7Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      2.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc     1.1Mb
    fonts   1.5Mb
    libs    2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    lib    6.6Mb
    libs   8.2Mb
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

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

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    include   2.9Mb
    libs      4.5Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
'LazyData' is specified without a 'data' directory
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    extdata  23.8Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs    4.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    rmd   8.0Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs       2.1Mb
    minizinc   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
GNU make is a SystemRequirements.
Found the following significant warnings:
  RlibMVL.c:1446:9: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.1/RMVL.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
Missing or unexported object: 'SummarizedExperiment::colnames'
Package suggested but not available for checking: 'rnaturalearthhires'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doxygen   1.4Mb
    libs      3.0Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/RobLoxBioC.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/RoBTT.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              4.2Mb
    simulationStudy   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
evalMedian: no visible global function definition for 'xtabs'
evalMode: no visible global function definition for 'xtabs'
rpartScore: no visible global function definition for 'model.extract'
rpartScore: no visible global function definition for 'var'
rpartScore: no visible binding for global variable 'var'
splitAbs: no visible global function definition for 'xtabs'
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in 'rpinterest-Ex.R' failed
The error most likely occurred in:

> ### Name: BoardPinsByID
> ### Title: Get board pins using board ID
> ### Aliases: BoardPinsByID
> 
> ### ** Examples
> 
> BoardPinsByID(boardID = "42080646457333782", token = "your_token")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [api.pinterest.com] Connection timed out after 10007 milliseconds
Calls: BoardPinsByID ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
Running examples in 'rpubs-Ex.R' failed
The error most likely occurred in:

> ### Name: extractCode-deprecated
> ### Title: Extract Code From Rpubs Article
> ### Aliases: extractCode-deprecated extractCode
> 
> ### ** Examples
> 
> extractCode(url = "http://rpubs.com/aephidayatuloh/sendgmail", file = NULL, output = FALSE)
Warning: 'extractCode()' will be removed in the next version
Use 'rpubs_code()' instead
Error in open.connection(x, "rb") : HTTP error 502.
Calls: extractCode -> read_html -> read_html.default
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
GNU make is a SystemRequirements.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.1/Rserve/libs/i386/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/4.1/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_Rmainloop'

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Name: SolrList-class
> ### Title: SolrList
> ### Aliases: class:SolrList SolrList-class length,SolrList-method
> ###   names,SolrList-method [<-,SolrList,ANY,ANY,ANY-method
> ###   [[,SolrList,ANY-method [,SolrList-method [[,SolrList-method
> ###   [[<-,SolrList-method unique,SolrList-method searchDocs
> ###   searchDocs,Solr SolrList coerce,Solr,SolrList-method
> ###   coerce,SolrList,DocCollection-method show,SolrList-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  4.68 0.12 4.82 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Running examples in 'rsparse-Ex.R' failed
The error most likely occurred in:

> ### Name: WRMF
> ### Title: Weighted Regularized Matrix Factorization for collaborative
> ###   filtering
> ### Aliases: WRMF
> 
> ### ** Examples
> 
> data('movielens100k')
> train = movielens100k[1:900, ]
> cv = movielens100k[901:nrow(movielens100k), ]
> model = WRMF$new(rank = 5,  lambda = 0, feedback = 'implicit')
> user_emb = model$fit_transform(train, n_iter = 5, convergence_tol = -1)
Error in library.dynam(lib, package, package.lib) : 
  DLL 'MatrixExtra' not found: maybe not installed for this architecture?
Calls: <Anonymous> -> loadNamespace -> library.dynam
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(rsparse)
  Loading required package: Matrix
  > library(data.table)
  > library(Matrix)
  > options(rsparse_omp_threads = 1L)
  > logger = lgr::get_logger('rsparse')
  > logger$set_threshold('warn')
  > data("movielens100k")
  > test_check("rsparse")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 44 ]
  
  == Failed tests ================================================================
  -- Error (test-wrmf.R:49:5): test WRMF core ------------------------------------
  Error in `library.dynam(lib, package, package.lib)`: DLL 'MatrixExtra' not found: maybe not installed for this architecture?
  Backtrace:
      x
   1. +-model$fit_transform(train, n_iter = 5, convergence_tol = -1) at test-wrmf.R:49:4
   2. \-base::loadNamespace(x)
   3.   \-base::library.dynam(lib, package, package.lib)
  -- Error (test-wrmf.R:86:5): test WRMF FLOAT -----------------------------------
  Error in `library.dynam(lib, package, package.lib)`: DLL 'MatrixExtra' not found: maybe not installed for this architecture?
  Backtrace:
      x
   1. +-model$fit_transform(train, n_iter = 5, convergence_tol = -1) at test-wrmf.R:86:4
   2. \-base::loadNamespace(x)
   3.   \-base::library.dynam(lib, package, package.lib)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 44 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.2Mb
    help   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/RSQLite.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.8Mb
    libs  17.4Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    lib    3.8Mb
    libs   9.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    libs  29.7Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

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

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   3.8Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: list_places -> <Anonymous> -> curlPerform -> <Anonymous> -> fun
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

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

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   2.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs     6.7Mb
    models   1.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 113.2Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    gdal     2.2Mb
    libs    96.1Mb
    proj     8.7Mb
    sqlite   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'sglasso-Ex.R' failed
The error most likely occurred in:

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

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

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

> out.klcv <- klcv(out.sglasso_path, X)
Error in klcv(out.sglasso_path, X) : error in dpotrf or dpotri subroutine
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hydromad'
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    www   7.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

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

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

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

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/SIGN.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/simer.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: unable to re-encode 'Estimate.R' line 276
  Warning: unable to re-encode 'model_DualKc.R' lines 259, 268, 270, 368, 386
  Warning: unable to re-encode 'model_Single_Kc.R' lines 240, 388, 389
See 'd:/Rcompile/CRANpkg/local/4.1/simET.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.7Mb
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rPython'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.4Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'MafDb.1Kgenomes.phase3.GRCh38'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/snSMART.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     3.2Mb
    doc   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.1Mb
    libs   3.4Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.0Mb
Package suggested but not available for checking: 'r2cytoscape'
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      5.1Mb
'LazyData' is specified without a 'data' directory
Running 'test-all.R' [109s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'SpaDES.core'
  
  The following objects are masked from 'package:stats':
  
      end, start
  
  The following object is masked from 'package:utils':
  
      citation
  
  trying URL 'https://www.zotero.org/styles/ecology-letters'
    adding: test.qs (stored 0%)
    adding: TransferFolder/cache.db (stored 0%)
    adding: TransferFolder/yCRp86x.grd (deflated 31%)
    adding: TransferFolder/yCRp86x.gri (deflated 55%)
    adding: TransferFolder/yCRp86x_1.grd (deflated 31%)
    adding: TransferFolder/yCRp86x_1.gri (deflated 55%)
    adding: TransferFolder/yCRp86x_2.grd (deflated 31%)
    adding: TransferFolder/yCRp86x_2.gri (deflated 55%)
    adding: temp/RtmpoVFxe6/JHJXYi/landscape_month1.rds (stored 0%)
  [ FAIL 1 | WARN 0 | SKIP 21 | PASS 651 ]
  
  == Skipped tests ===============================================================
  * On CRAN (12)
  * On Windows (1)
  * benchmarking DES (1)
  * empty test (4)
  * interactive() is not TRUE (1)
  * restartR not possible in automated tests (1)
  * restartR with logging not possible in automated tests (1)
  
  == Failed tests ================================================================
  -- Error (<text>:6:3): module templates work -----------------------------------
  Error in `download.file("https://www.zotero.org/styles/ecology-letters", 
      destfile = "citations/ecology-letters.csl")`: cannot open URL 'https://www.zotero.org/styles/ecology-letters'
  Backtrace:
      x
   1. \-utils::download.file(...)
  
  [ FAIL 1 | WARN 0 | SKIP 21 | PASS 651 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   3.1Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    java   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'spatialEco-Ex.R' failed
The error most likely occurred in:

> ### Name: cgls_urls
> ### Title: Provide URL's for Copernicus Global Land Service datasets
> ### Aliases: cgls_urls
> 
> ### ** Examples
> 
> # Create date string for query
> d <- seq(as.Date("2020/05/01"), as.Date("2020-09-01"), by="day")
> 
> # Search for 300m (333m) LAI within specified date range 
> all.urls <- cgls_urls(dates = d, resolution = 300, 
+                         product = "lai")		
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: cgls_urls -> paste -> readLines -> file
Execution halted
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   2.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    help   2.8Mb
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet', 'spatstat.data', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
    etc   1.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs      3.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

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

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'squat-Ex.R' failed
The error most likely occurred in:

> ### Name: smooth_qts
> ### Title: QTS Smoothing via SLERP Interpolation
> ### Aliases: smooth_qts
> 
> ### ** Examples
> 
> smooth_qts(vespa64$igp[[1]])
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(squat)
  > 
  > test_check("squat")
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.3Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'SRTsim.Rmd' using rmarkdown
Quitting from lines 26-47 (SRTsim.Rmd) 
Error: processing vignette 'SRTsim.Rmd' failed with diagnostics:
there is no package called 'BiocFileCache'
--- failed re-building 'SRTsim.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/SSDforR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  21.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/stableGR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    include   9.7Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'starsdata'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   1.7Mb
    nc    1.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.7Mb
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      2.5Mb
Package suggested but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
Data codoc mismatches from documentation object 'SLCS':
Variables in data frame 'SLCS'
  Code: SLCS_1 SLCS_10 SLCS_11 SLCS_12 SLCS_13 SLCS_14 SLCS_15 SLCS_16
        SLCS_2 SLCS_3 SLCS_4 SLCS_5 SLCS_6 SLCS_7 SLCS_8 SLCS_9 age sex
        user_id
  Docs: SLCS_11 SLCS_1 SLCS_10 SLCS_12 SLCS_13 SLCS_14 SLCS_15 SLCS_16
        SLCS_2 SLCS_3 SLCS_4 SLCS_5 SLCS_6 SLCS_7 SLCS_8 SLCS_9 age sex
        user_id
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.4Mb
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installed size is 21.1Mb
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installed size is  7.0Mb
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
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installed size is  6.1Mb
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Malformed Title field: should not end in a period.
Package required and available but unsuitable version: 'stringi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/string2path.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/stringi.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'STRaitRazoR'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.5Mb
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installed size is 13.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
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installed size is  6.4Mb
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GNU make is a SystemRequirements.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
installed size is 15.6Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.4Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'swephRdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cplexAPI'
Package suggested but not available for checking: 'cplexAPI'
installed size is  5.1Mb
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Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
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Error(s) in re-building vignettes:
--- re-building 'quickstart_tutorial.Rmd' using rmarkdown
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Quitting from lines 144-155 (quickstart_tutorial.Rmd) 
Error: processing vignette 'quickstart_tutorial.Rmd' failed with diagnostics:
element-wise pow(): incompatible matrix dimensions: 100x2 and 2x1
--- failed re-building 'quickstart_tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'unix'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tashudata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    apps   1.3Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       3.7Mb
    libs      2.2Mb
    telemac   1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
installed size is 114.0Mb
  sub-directories of 1Mb or more:
    R       1.8Mb
    gdal    2.2Mb
    libs  100.2Mb
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installed size is 29.7Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.0Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
--- re-building 'huggingface_in_r.Rmd' using rmarkdown
Error: processing vignette 'huggingface_in_r.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'huggingface_in_r.Rmd'

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

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

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

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

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

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

SUMMARY: processing the following files failed:
  'huggingface_in_r.Rmd' 'huggingface_in_r_and_computer_capacity.Rmd'
  'pre-registration_and_transformers.Rmd'
  'removing_huggingface_transformers_cache_files.Rmd'
  'singularity_transformers_container.Rmd' 'text.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
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    libs      2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
Error(s) in re-building vignettes:
--- re-building 'theft.Rmd' using rmarkdown
No IDs removed. All value vectors good for feature extraction.
Running computations for catch22...
Warning: As of 0.1.14 the feature 'CO_f1ecac' returns a double instead of int
This warning is displayed once per session.

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    data   3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
GNU make is a SystemRequirements.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    test_db   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   4.4Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   1.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   5.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'TKCat-User-guide.Rmd' using rmarkdown
Loading required package: ReDaMoR
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: magrittr
Loading required package: visNetwork

Attaching package: 'ReDaMoR'

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

    lengths

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

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

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

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

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

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

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

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

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

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

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

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taxidata'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  20.4Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'V01_get_started.Rmd' using rmarkdown
Loading required package: stars
Loading required package: abind
Loading required package: sf
Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 7.2.1; sf_use_s2() is TRUE
--- finished re-building 'V01_get_started.Rmd'

--- re-building 'V02_inputs_preparation_stars.Rmd' using rmarkdown
Loading required package: stars
Loading required package: abind
Loading required package: sf
Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 7.2.1; sf_use_s2() is TRUE
udunits database from D:/temp/RtmpCMslsK/RLIBS_1520676f14/units/share/udunits/udunits2.xml
--- finished re-building 'V02_inputs_preparation_stars.Rmd'

--- re-building 'V03_inputs_preparation_whitebox.Rmd' using rmarkdown
Quitting from lines 45-66 (V03_inputs_preparation_whitebox.Rmd) 
Error: processing vignette 'V03_inputs_preparation_whitebox.Rmd' failed with diagnostics:
there is no package called 'rgdal'
--- failed re-building 'V03_inputs_preparation_whitebox.Rmd'

SUMMARY: processing the following file failed:
  'V03_inputs_preparation_whitebox.Rmd'

Error: Vignette re-building failed.
Execution halted
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'TreeDistData'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    libs       2.2Mb
'LazyData' is specified without a 'data' directory
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/tweetcheck.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'sl3'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     7.0Mb
    ubinc   2.0Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   7.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  23.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'USAboundariesData'
Package suggested but not available for checking: 'USA.state.boundaries.data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(usincometaxes)
  > 
  > test_check("usincometaxes")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 9 ]
  
  == Failed tests ================================================================
  -- Error ('test-calculate_taxes.R:98'): All interface options return same values --
  Error: There was a problem in calculating the taxes using 'ssh'.
  Please try a different `interface` option.
  Alternatively, you can try manually uploading the data to TAXSIM as an avenue of troubleshooting.
  See the following address for more information: https://www.shaneorr.io/r/usincometaxes/articles/send-data-to-taxsim.html
  Backtrace:
      x
   1. \-usincometaxes::taxsim_calculate_taxes(...) at test-calculate_taxes.R:98:2
   2.   \-base::tryCatch(...)
   3.     \-base (local) tryCatchList(expr, classes, parentenv, handlers)
   4.       \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5.         \-value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 9 ]
  Error: Test failures
  Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   6.6Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  23.2Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   5.0Mb
Running 'testthat.R' [21s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(VAJointSurv)
  Loading required package: survival
  > 
  > options(testthat.progress.max_fails = 1000)
  > test_check("VAJointSurv")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 6094 ]
  
  == Skipped tests ===============================================================
  * On CRAN (3)
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 6094 ]
  > 
  > proc.time()
     user  system elapsed 
    20.13    0.35   20.70 
  Error: bad value
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: 'h3jsr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'VedicDateTime.Rmd' using rmarkdown
Error: processing vignette 'VedicDateTime.Rmd' failed with diagnostics:
Using a custom highlighting style requires Pandoc 2.0 and above
--- failed re-building 'VedicDateTime.Rmd'

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

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

> ### Name: from_spec
> ### Title: Take a JSON Vega-Lite Spec and render as an htmlwidget
> ### Aliases: from_spec
> 
> ### ** Examples
> 
> from_spec("http://rud.is/dl/embedded.json")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung wurde zurückgesetzt.'
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    help   2.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    ext   4.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   8.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    6.3Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Package suggested but not available for checking: 'prepr'
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

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

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

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

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

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

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

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

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'wikiTools-Ex.R' failed
The error most likely occurred in:

> ### Name: extractWiki
> ### Title: Extract the first paragraph of a Wikipedia article with a
> ###   maximum of characters.
> ### Aliases: extractWiki
> 
> ### ** Examples
> 
> ## Obtaining information in English Wikidata
> names <- c("William Shakespeare", "Pablo Picasso")
> info <- getWikiInf(names)
> info$text <- extractWiki(info$label)
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: extractWiki ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
'LazyData' is specified without a 'data' directory
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

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

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

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

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

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

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

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

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(zipangu)
  > 
  > test_check("zipangu")
  [ FAIL 3 | WARN 16 | SKIP 2 | PASS 142 ]
  
  == Skipped tests ===============================================================
  * On CRAN (2)
  
  == Failed tests ================================================================
  -- Failure (test-jyear.R:10:3): convert jyear works ----------------------------
  convert_jyear("<U+5E73><U+6210><U+5143><U+5E74>") not equal to convert_jyear("H1").
  1/1 mismatches
  [1] NA - 1989 == NA
  -- Failure (test-jyear.R:33:3): convert japanese date format -------------------
  convert_jdate("<U+4EE4><U+548C>2<U+5E74>7<U+6708>6<U+65E5>") not equal to as.Date("2020-07-06").
  'is.NA' value mismatch: 0 in current 1 in target
  -- Failure (test-jyear.R:45:3): convert japanese date format -------------------
  convert_jdate(...) not equal to as.Date(c("2018-01-01", "2018-02-01", NA)).
  'is.NA' value mismatch: 1 in current 3 in target
  
  [ FAIL 3 | WARN 16 | SKIP 2 | PASS 142 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'zdat'
Running examples in 'zoon-Ex.R' failed
The error most likely occurred in:

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