Maintainer: ‘Hans Peter Wolf <pwolf@wiwi.uni-bielefeld.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Hans", "Peter"),
                    family = "Wolf",
                    role = c("aut", "cre"),
                    email = "pwolf@wiwi.uni-bielefeld.de")
as necessary.
checkRd: (-1) iconplot.Rd:172: Lost braces
   172 |     the height of the area containing the panels and a margin of size code{100 * 0.1} 
       |                                                                           ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'flextable', 'arsenal'

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Quinten Stokkink <q.a.stokkink@tudelft.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Quinten",
                    family = "Stokkink",
                    role = c("aut", "cre"),
                    email = "q.a.stokkink@tudelft.nl")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Found the following calls to attach():
File ‘apollo/R/apollo_attach.R’:
  attach(as.list(apollo_beta), warn.conflicts = FALSE)
  attach(database, warn.conflicts = FALSE)
  attach(draws, warn.conflicts = FALSE)
  attach(randcoeff, warn.conflicts = FALSE)
  attach(lcpars, warn.conflicts = FALSE)
See section ‘Good practice’ in ‘?attach’.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Package required but not available: ‘keyring’

Packages suggested but not available for checking:
  'rmarkdown', 'covr', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Eisuke Inoue <eisuke.inoue@marianna-u.ac.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Eisuke",
                      family = "Inoue",
                      role = c("aut", "cre"),
                      email = "eisuke.inoue@marianna-u.ac.jp"),
               person(given = "Hajime",
                      family = "Uno",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Max Kuhn <mxkuhn@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Max",
                      family = "Kuhn",
                      role = c("aut", "cre"),
                      email = "mxkuhn@gmail.com"),
               person(given = "Kjell",
                      family = "Johnson",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'DT', 'rhandsontable', 'sortable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Robin K. S. Hankin <hankin.robin@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Robin", "K.", "S."),
                    family = "Hankin",
                    role = c("aut", "cre"),
                    email = "hankin.robin@gmail.com")
as necessary.
Maintainer: ‘Bikram Karmakar <bkarmakar@ufl.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bikram",
                    family = "Karmakar",
                    role = c("aut", "cre"),
                    email = "bkarmakar@ufl.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Marco D. Visser <marco.d.visser@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Marco", "D."),
                    family = "Visser",
                    role = c("aut", "cre"),
                    email = "marco.d.visser@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Packages suggested but not available for checking:
  'BayesianTools', 'listviewer', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Hengrui Cai <hengruicai@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hengrui",
                      family = "Cai",
                      role = c("aut", "cre"),
                      email = "hengruicai@gmail.com"),
               person(given = "Yan",
                      family = "Yuan",
                      role = "aut",
                      email = "yyuan@ualberta.ca"),
               person(given = c("Qian", "Michelle"),
                      family = "Zhou",
                      role = "aut",
                      email = "qz70@msstate.edu"),
               person(given = "Bingying",
                      family = "Li",
                      role = "aut",
                      email = "dorisli1120@gmail.com"))
as necessary.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘loa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘John Lawson <lawsonjsl7net@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "John",
                    family = "Lawson",
                    role = c("aut", "cre"),
                    email = "lawsonjsl7net@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'Hmisc', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'learnr', 'prettydoc', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'devtools', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Karline Soetaert <Karline.Soetaert@nioz.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Andreas", "F."),
                      family = "Hofmann",
                      role = "aut"),
               person(given = "Karline",
                      family = "Soetaert",
                      role = c("aut", "cre"),
                      email = "karline.soetaert@nioz.nl"),
               person(given = c("Filip", "J.R."),
                      family = "Meysman",
                      role = "aut"),
               person(given = "Mathilde",
                      family = "Hagens",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘rlist’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Rich Nielsen <rnielsen@mit.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Rich",
                    family = "Nielsen",
                    role = c("aut", "cre"),
                    email = "rnielsen@mit.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                              ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                                            ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'ArchaeoData', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘David L. Carlson <dcarlson@tamu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("David", "L."),
                      family = "Carlson",
                      role = c("aut", "cre"),
                      email = "dcarlson@tamu.edu"),
               person(given = "Georg",
                      family = "Roth",
                      role = "ctb"))
as necessary.
Package required but not available: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'plotly', 'htmlwidgets', 'knitr'

Packages suggested but not available for checking:
  'covr', 'SEAHORS', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael Korvink <mkorvink@protonmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available:
  'knitr', 'config', 'tidyverse', 'rmarkdown', 'skimr'

Packages suggested but not available for checking:
  'covr', 'gtsummary', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Benjamin M Delory <Benjamin.Delory@leuphana.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Benjamin", "M"),
                      family = "Delory",
                      role = c("aut", "cre"),
                      email = "benjamin.delory@leuphana.de"),
               person(given = "Caroline",
                      family = "Baudson",
                      role = "aut"),
               person(given = "Yves",
                      family = "Brostaux",
                      role = "aut"),
               person(given = "Guillaume",
                      family = "Lobet",
                      role = "aut"),
               person(given = c("Patrick", "du"),
                      family = "Jardin",
                      role = "aut"),
               person(given = "Loic",
                      family = "Pages",
                      role = "aut"),
               person(given = "Pierre",
                      family = "Delaplace",
                      role = "aut"))
as necessary.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(archiveRetriever)
  > 
  > test_check("archiveRetriever")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-archiveRetriever.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("archiveRetriever")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at ./setup-archiveRetriever.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Running examples in ‘archivist-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ahistory
> ### Title: Show Artifact's History
> ### Aliases: ahistory
> 
> ### ** Examples
> 
> 
> createLocalRepo("ahistory_check", default = TRUE)
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> iris %a%
+ filter(Sepal.Length < 6) %a%
+  lm(Petal.Length~Species, data=.) %a%
+  summary() -> artifact
Error in saveToRepo(env[[nm]], archiveData = FALSE, artifactName = lhs_name) : 
  devtools package required for archiveSessionInfo parameter
Calls: %a% ... eval -> %a% -> eval -> eval -> %a% -> paste0 -> saveToRepo
Execution halted
'library' or 'require' call not declared from: ‘gridExtra’
Found the following files/directories:
  ‘ahistory_check’
Maintainer: ‘Pulong Ma <mpulong@gmail.com>’

The Description field contains
  Andrew T Cox (2019) <arXiv:1909.01836>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Specified C++11: support will be removed soon
checkRd: (-1) estimate_t0.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:75: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘DT’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Marta Karas <marta.karass@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Maintainer: ‘Susana Barbosa <sabarbosa@fc.ul.pt>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Susana",
                    family = "Barbosa",
                    role = c("aut", "cre"),
                    email = "sabarbosa@fc.ul.pt")
as necessary.
Package required but not available: ‘rlist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       | ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                 ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                                ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |   ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                  ^
checkRd: (-1) uecm.Rd:76-77: Lost braces
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                                             ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘ontologics’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Christopher Prener <chris.prener@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘gistr’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pkgdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'colourpicker', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tidyverse’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘David J. H. Shih <djh.shih@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("David", "J.", "H."),
                    family = "Shih",
                    role = c("aut", "cre"),
                    email = "djh.shih@gmail.com")
as necessary.
'library' or 'require' call not declared from: ‘magrittr’
Maintainer: ‘Haoran Li <hrli@ucdavis.edu>’

The Description field contains
  by Li et al., (2016) <arXiv:1609.08725>. Both one-sample and two-sample
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Livio Finos <livio.finos@unipd.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Livio",
                      family = "Finos",
                      role = c("aut", "cre"),
                      email = "livio.finos@unipd.it"),
               person(given = "Jelle",
                      family = "Goeman",
                      role = "aut"),
               person(given = "Wouter",
                      family = "Weeda",
                      role = "aut"),
               person(given = "Jonathan",
                      family = "Rosenblatt",
                      role = "aut"),
               person(given = "Aldo",
                      family = "Solari",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'DescribeDF', 'fGarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'text2speech', 'rmarkdown'

Packages suggested but not available for checking: 'xaringan', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'tensorflow', 'keras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ar.matrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.iid
> ### Title: Precision matrix for a IID process
> ### Aliases: Q.iid r.iid
> 
> ### ** Examples
> 
> require("leaflet")
Loading required package: leaflet
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘leaflet’
> require("sp")
Loading required package: sp
> 
> # simulate iid data and attach to spatial polygons data frame
> US.df@data$data <- c(r.iid(1, M=nrow(US.graph), sigma=1))
> 
> # color palette of data
> pal <- colorNumeric(palette="YlGnBu", domain=US.df@data$data)
Error in colorNumeric(palette = "YlGnBu", domain = US.df@data$data) : 
  could not find function "colorNumeric"
Execution halted
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Antonio Profico <antonio.profico@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Antonio",
                      family = "Profico",
                      role = c("aut", "cre"),
                      email = "antonio.profico@gmail.com"),
               person(given = "Costantino",
                      family = "Buzi",
                      role = "aut"),
               person(given = "Silvia",
                      family = "Castiglione",
                      role = "aut"),
               person(given = "Marina",
                      family = "Melchionna",
                      role = "aut"),
               person(given = "Paolo",
                      family = "Piras",
                      role = "aut"),
               person(given = "Pasquale",
                      family = "Raia",
                      role = "aut"),
               person(given = "Alessio",
                      family = "Veneziano",
                      role = "aut"))
as necessary.
Packages required but not available: 'alphashape3d', 'Morpho', 'rgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘James E. Pustejovsky <jepusto@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("James", "E."),
                      family = "Pustejovsky",
                      role = c("aut", "cre"),
                      email = "jepusto@gmail.com"),
               person(given = c("with", "contributions", "from", "Daniel", "M."),
                      family = "Swan",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘C. Beleites <claudia.beleites@chemometrix.eu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "C.",
                    family = "Beleites",
                    role = c("aut", "cre"),
                    email = "claudia.beleites@chemometrix.eu")
as necessary.
Maintainer: ‘Abbas Parchami <parchami@uk.ac.ir>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Abbas",
                    family = "Parchami",
                    role = c("aut", "cre"),
                    email = "parchami@uk.ac.ir",
                    comment = "Department of Statistics, Faculty of Mathematics and Computer, Shahid Bahonar University of Kerman, Kerman, Iran")
as necessary.
Package required but not available: ‘knitr’

Packages suggested but not available for checking: 'rmarkdown', 'yaml'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lintr', 'tidyverse', 'usethis', 'yaml'

Packages suggested but not available for checking:
  'box.linters', 'covr', 'devtools', 'knitr', 'languageserver',
  'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Pablo J. Villacorta <pjvi@decsai.ugr.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Pablo", "J."),
                    family = "Villacorta",
                    role = c("aut", "cre"),
                    email = "pjvi@decsai.ugr.es")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael Hahsler <mhahsler@lyle.smu.edu>’

The BugReports field in DESCRIPTION has
  https://github.com/mhahsler/arulesNBMiner
which should likely be
  https://github.com/mhahsler/arulesNBMiner/issues
instead.
Package required but not available: ‘rJava’

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

Package suggested but not available for checking: ‘htmlwidgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Dirk F. Moore <dirkfmoore@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Dirk", "F."),
                    family = "Moore",
                    role = c("aut", "cre"),
                    email = "dirkfmoore@gmail.com")
as necessary.
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Maintainer: ‘Brian <bleemayer@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Brian", "Lee"),
                      family = "Mayer",
                      role = "aut"),
               person(family = "Brian",
                      role = "cre",
                      email = "bleemayer@gmail.com"))
as necessary.
Maintainer: ‘Jeremy Leipzig <leipzig@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jeremy",
                    family = "Leipzig",
                    role = c("aut", "cre"),
                    email = "leipzig@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Nick Parsons <nick.parsons@warwick.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nick",
                    family = "Parsons",
                    role = c("aut", "cre"),
                    email = "nick.parsons@warwick.ac.uk")
as necessary.
Package required but not available: ‘alphashape3d’

Packages suggested but not available for checking:
  'knitr', 'rgl', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Albrecht Gebhardt <albrecht.gebhardt@aau.at>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("S", "original", "by", "David", "W.", "Scott", "R", "port", "by", "Albrecht", "Gebhardt", "adopted", "to", "recent", "S-PLUS", "by", "Stephen", "Kaluzny"),
                      family = "<spk@insightful.com>",
                      role = "aut",
                      email = "spk@insightful.com"),
               person(given = "Albrecht",
                      family = "Gebhardt",
                      role = "cre",
                      email = "albrecht.gebhardt@aau.at"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'llama', 'RWeka', 'yaml'

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

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/asmapvignette.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Damien R. Farine <dfarine@ab.mpg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Damien", "R."),
                    family = "Farine",
                    role = c("aut", "cre"),
                    email = "dfarine@ab.mpg.de")
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Matt Wayland <mw283@cam.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Matt",
                    family = "Wayland",
                    role = c("aut", "cre"),
                    email = "mw283@cam.ac.uk")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Vivien Goepp <vivien.goepp@gmail.com>’

The Description field contains
  Selection", <arXiv:1808.01770>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Il-Youp Kwak <ikwak2@cau.ac.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Il-Youp",
                      family = "Kwak",
                      role = c("aut", "cre"),
                      email = "ikwak2@cau.ac.kr"),
               person(given = c("others", "in", "each", "function"),
                      family = "manual)",
                      role = "aut",
                      comment = "s"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘devtools’

Package which this enhances but not available for checking: ‘asreml’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Miguel de Carvalho <miguel.decarvalho@ed.ac.uk>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'visNetwork', 'covr', 'flextable', 'knitr', 'roxygen2'

Package suggested but not available for checking: ‘colourpicker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rolf Turner <r.turner@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Rolf",
                    family = "Turner",
                    role = c("aut", "cre"),
                    email = "r.turner@auckland.ac.nz")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) plot.AssetPricing.Rd:199-200: Lost braces
   199 |   yakka. (Note that \code{flap} stands for dQuote{function list
       |                                                  ^
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Damien Farine <dfarine@orn.mpg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "William",
                      family = "Hoppitt",
                      role = "aut"),
               person(given = "Damien",
                      family = "Farine",
                      role = c("aut", "cre"),
                      email = "dfarine@orn.mpg.de"))
as necessary.
Maintainer: ‘Damien Farine <damien.farine@anu.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Damien",
                    family = "Farine",
                    role = c("aut", "cre"),
                    email = "damien.farine@anu.edu.au")
as necessary.
Packages required but not available:
  'tidyverse', 'knitr', 'MVN', 'DHARMa', 'DT', 'kableExtra', 'sjPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'asteRiskData', 'knitr', 'BiocStyle', 'plotly', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Error(s) in re-building vignettes:
  ...
--- re-building ‘delta.Rnw’ using Sweave
Error: processing vignette 'delta.Rnw' failed with diagnostics:
at delta.Rnw:55, there is no package called ‘knitr’
--- failed re-building ‘delta.Rnw’

--- re-building ‘linkingTo.Rnw’ using Sweave
--- finished re-building ‘linkingTo.Rnw’

--- re-building ‘re.Rnw’ using Sweave
--- finished re-building ‘re.Rnw’

--- re-building ‘trunc.Rnw’ using Sweave
--- finished re-building ‘trunc.Rnw’

--- re-building ‘tutor.Rnw’ using Sweave
--- finished re-building ‘tutor.Rnw’

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ali Ghanbari  <a.ghanbari541@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Parinaz",
                      family = "Mehdipour",
                      role = "aut",
                      email = "mehdipoor.p@gmail.com"),
               person(given = "Ali",
                      family = "Ghanbari",
                      role = c("cre", "aut"),
                      email = "a.ghanbari541@gmail.com"),
               person(given = "Farshad",
                      family = "Farzadfar",
                      role = "cph",
                      email = "farzadfar3@yahoo.com"))
as necessary.
Maintainer: ‘Andrew Harris <harris@astro.umd.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andrew",
                    family = "Harris",
                    role = c("aut", "cre"),
                    email = "harris@astro.umd.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Richard M. Single <rsingle@uvm.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Richard", "M."),
                    family = "Single",
                    role = c("aut", "cre"),
                    email = "rsingle@uvm.edu")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Running examples in ‘asymLD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute.ALD
> ### Title: Compute ALD.
> ### Aliases: compute.ALD
> 
> ### ** Examples
> 
> library(asymLD)
> 
> # An example using haplotype frequencies from Wilson(2010)
> data(hla.freqs)
> hla.a_b <- hla.freqs[hla.freqs$locus1=="A" & hla.freqs$locus2=="B",]
> compute.ALD(hla.a_b)
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2       F.1    F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      A      B 0.1021811 0.340332 0.04876543 0.1903394 0.5150291 0.3857872
> hla.freqs$locus <- paste(hla.freqs$locus1, hla.freqs$locus2, sep="-")
> compute.ALD(hla.freqs[hla.freqs$locus=="C-B",])
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2        F.1     F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      C      B 0.08637241 0.7350216 0.05040254 0.4520268 0.8425979 0.6503396
> # Note: additonal columns on the input dataframe (e.g., "locus" above) are allowed, but
> # ignored by the function.
> 
> # An example using genotype data from the haplo.stats package
> require(haplo.stats)
Loading required package: haplo.stats
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘haplo.stats’
> data(hla.demo)
Warning in data(hla.demo) : data set ‘hla.demo’ not found
> geno <- hla.demo[,5:8]  #DPB-DPA
Error: object 'hla.demo' not found
Execution halted
Package required but not available: ‘smacof’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Pierre Lafaye de Micheaux <lafaye@unsw.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Cqls",
                      family = "Team",
                      role = "aut"),
               person(given = c("Pierre", "Lafaye"),
                      family = "de Micheaux",
                      role = "cre",
                      email = "lafaye@unsw.edu.au"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/atable_usage.rnw’
   ‘inst/doc/extending.Rnw’
   ‘inst/doc/modifying.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                       ^
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                                                ^
'library' or 'require' call not declared from: ‘sp’
Maintainer: ‘Sokbae Lee <sl3841@columbia.edu>’

The Description field contains
  Pooling Limited Information across Observations," <arXiv:2111.05243>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) simulation_dgp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{x_discrete}{TRUE if the distribution of the covariate is uniform on {-3.0, -2.9, ..., 3.0} and
       |                                                                           ^
checkRd: (-1) simulation_dgp.Rd:23: Lost braces
    23 | \item{att_oracle}{the sample analog of E[D{Y(1) - Y(0)}|D=1]}
       |                                           ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rStrava’

Packages suggested but not available for checking:
  'devtools', 'knitr', 'pkgdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘leaflet’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Vladimir Polony <podalv@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Vladimir",
                    family = "Polony",
                    role = c("aut", "cre"),
                    email = "podalv@gmail.com")
as necessary.
Packages required but not available: 'plotly', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Simon Mak <smak6@gatech.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Simon",
                    family = "Mak",
                    role = c("aut", "cre"),
                    email = "smak6@gatech.edu")
as necessary.

The Description field contains
  <arXiv:1712.03589>. This work was supported by USARO grant
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘atmopt-package.Rd’:
    \keyword{ Robust optimization, discrete optimizati [TRUNCATED]
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Packages required but not available: 'rdflib', 'keyring'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘atpol_grids.R’ ‘miscRscript.r’ ‘plot_points_on_atpol.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘catchment_sim.R’ ‘elementary_pop.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Debin Qiu <debinqiu@uga.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Debin",
                    family = "Qiu",
                    role = c("aut", "cre"),
                    email = "debinqiu@uga.edu")
as necessary.
Packages required but not available:
  'knitr', 'rmarkdown', 'roxygen2', 'yaml'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jonas Moss <jonas.gjertsen@gmail.com>’

The Description field contains
  Implements the methods described in Moss (2019, <arxiv:1911.01576>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michel Ballings <Michel.Ballings@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michel",
                      family = "Ballings",
                      role = c("aut", "cre"),
                      email = "michel.ballings@gmail.com"),
               person(given = "Dirk",
                      family = "Van den Poel",
                      role = "aut"))
as necessary.
Maintainer: ‘Josh Gardner <jpgard@umich.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Bernhard Lehnert <bernhard.lehnert@med.uni-greifswald.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bernhard",
                    family = "Lehnert",
                    role = c("aut", "cre"),
                    email = "bernhard.lehnert@med.uni-greifswald.de")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘gg_freiburg.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Simon Urbanek <simon.urbanek@r-project.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Simon",
                    family = "Urbanek",
                    role = c("aut", "cre"),
                    email = "simon.urbanek@r-project.org")
as necessary.
checkRd: (-1) audioSample.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) audioSample.Rd:21: Lost braces in \itemize; meant \describe ?
File ‘audio/libs/audio.so’:
  Found non-API calls to R: ‘EXTPTR_PTR’, ‘R_checkActivity’
This entry point may be removed soon:
‘EXTPTR_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'r2d3', 'rmarkdown', 'spelling', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘auditor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotD3
> ### Title: Model Diagnostic Plots in D3 with r2d3 package.
> ### Aliases: plotD3 plotD3_auditor plotD3.auditor_model_residual
> ###   plotD3.auditor_model_halfnormal plotD3.auditor_model_evaluation
> ###   plotD3.auditor_model_cooksdistance
> 
> ### ** Examples
> 
> dragons <- DALEX::dragons[1:100, ]
> 
> # fit a model
> model_lm <- lm(life_length ~ ., data = dragons)
> 
> lm_audit <- audit(model_lm, data = dragons, y = dragons$life_length)
Preparation of a new explainer is initiated
  -> model label       :  lm  ( [33m default [39m )
  -> data              :  100  rows  8  cols 
  -> target variable   :  100  values 
  -> predict function  :  yhat.lm  will be used ( [33m default [39m )
  -> predicted values  :  No value for predict function target column. ( [33m default [39m )
  -> model_info        :  package stats , ver. 4.6.0 , task regression ( [33m default [39m ) 
  -> predicted values  :  numerical, min =  585.8311 , mean =  1347.787 , max =  2942.307  
  -> residual function :  difference between y and yhat ( [33m default [39m )
  -> residuals         :  numerical, min =  -88.41755 , mean =  -1.796256e-13 , max =  77.92805  
 [32m A new explainer has been created! [39m 
> 
> # validate a model with auditor
> mr_lm <- model_residual(lm_audit)
> 
> # plot results
> plotD3(mr_lm)
Error in loadNamespace(x) : there is no package called ‘r2d3’
Calls: plotD3 ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Glen Meeden <glen@stat.umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Glen",
                      family = "Meeden.",
                      role = "aut",
                      email = "glen@stat.umn.edu"),
               person(given = "Glen",
                      family = "Meeden",
                      role = "cre",
                      email = "glen@stat.umn.edu"))
as necessary.
Maintainer: ‘Giancarlo Vercellino <giancarlo.vercellino@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Giancarlo",
                    family = "Vercellino",
                    role = c("aut", "cre"),
                    email = "giancarlo.vercellino@gmail.com")
as necessary.
Package required but not available: ‘modeest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bind_lr.Rd’ ‘lex_density.Rd’
Package required but not available: ‘flextable’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Qihuang Zhang <qihuang.zhang@uwaterloo.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Qihuang",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "qihuang.zhang@uwaterloo.ca"),
               person(given = c("Grace", "Y."),
                      family = "Yi",
                      role = "aut",
                      email = "yyi@uwaterloo.ca"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Aritra Banerjee <aritra306@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Aritra",
                    family = "Banerjee",
                    role = c("aut", "cre"),
                    email = "aritra306@gmail.com")
as necessary.
Maintainer: ‘Dai Feng <daifeng.stat@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dai",
                      family = "Feng",
                      role = c("aut", "cre"),
                      email = "daifeng.stat@gmail.com"),
               person(given = "Damjan",
                      family = "Manevski",
                      role = "auc"),
               person(given = c("Maja", "Pohar"),
                      family = "Perme",
                      role = "auc"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Arjun Sondhi <asondhi@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Arjun",
                      family = "Sondhi",
                      role = c("aut", "cre"),
                      email = "asondhi@uw.edu"),
               person(given = "Ken",
                      family = "Rice",
                      role = "aut"))
as necessary.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘yaml’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Vitor Cerqueira <cerqueira.vitormanuel@gmail.com>’

The Description field contains
  arXiv:1706.09367.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Dennis Robert <dennis.robert.nm@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dennis",
                    family = "Robert",
                    role = c("aut", "cre"),
                    email = "dennis.robert.nm@gmail.com")
as necessary.
checkRd: (-1) get_candidate_covariates.Rd:50: Lost braces
    50 | \item \code{covars_data}   {The \code{data.frame} that is filtered out of \code{df} with only the selected \code{covars}}. The values of the
       |                            ^
checkRd: (-1) get_candidate_covariates.Rd:53: Lost braces
    53 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
checkRd: (-1) get_prioritised_covariates.Rd:40: Lost braces
    40 | \item \code{multiplicative_bias}{The absolute log of the multiplicative bias term for each of the auto-selected prioritised covariates}
       |                                 ^
checkRd: (-1) get_recurrence_covariates.Rd:34: Lost braces
    34 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'DiagrammeR', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘ShengLi Tzeng <slt.cmu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "ShengLi",
                      family = "Tzeng",
                      role = c("aut", "cre"),
                      email = "slt.cmu@gmail.com"),
               person(given = "Hsin-Cheng",
                      family = "Huang",
                      role = "aut"),
               person(given = "Wen-Ting",
                      family = "Wang",
                      role = "ctb"),
               person(given = "Douglas",
                      family = "Nychka",
                      role = "ctb"),
               person(given = "Colin",
                      family = "Gillespie",
                      role = "ctb"))
as necessary.
Specified C++11: support will be removed soon
Package required but not available: ‘univariateML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Found the following significant warnings:
  Warning: namespace ‘ergm’ is not available and has been replaced
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/autograph.Rcheck/00install.out’ for details.
Packages required but not available: 'knitr', 'rmarkdown', 'lintr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Joshua French <joshua.french@ucdenver.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Joshua",
                    family = "French",
                    role = c("aut", "cre"),
                    email = "joshua.french@ucdenver.edu")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘diffviewer’

Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'tidyverse'

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

Package suggested but not available for checking: ‘covr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'EBMAforecast', 'knitr'

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

Package suggested but not available for checking: ‘lintr’

VignetteBuilder package required for checking but not installed: ‘quarto’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Navinkumar Nedunchezhian <navinkumar.nedunchezhian@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Navinkumar",
                    family = "Nedunchezhian",
                    role = c("aut", "cre"),
                    email = "navinkumar.nedunchezhian@gmail.com")
as necessary.
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yao Geng <gengyao0103521@qq.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xiaoyu",
                      family = "Zhang",
                      role = "aut"),
               person(given = "Yao",
                      family = "Geng",
                      role = "cre",
                      email = "gengyao0103521@qq.com"))
as necessary.
checkRd: (-1) Autoplotprotein-package.Rd:27: Lost braces
    27 | code{\link{help}}
       |     ^
checkRd: (-1) Autoplotprotein.Rd:25: Lost braces
    25 | code{\link{help}}
       |     ^
checkRd: (-1) data.Rd:22: Lost braces
    22 | code{\link{help}}
       |     ^
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
Packages required but not available:
  'echarts4r', 'quanteda', 'quanteda.textstats'

Package suggested but not available for checking: ‘spelling’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'survminer'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) noauto_scorecard.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{fit}{See glm {stats}.}
       |                    ^
checkRd: (-1) noauto_scorecard2.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{fit}{See glm {stats}.}
       |                    ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
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Packages required but not available:
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Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  'devtools', 'filters', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'flextable'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Aaron England <aaron.england24@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Aaron",
                    family = "England",
                    role = c("aut", "cre"),
                    email = "aaron.england24@gmail.com")
as necessary.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'keras', 'tensorflow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Vivien Roussez <vivien.roussez@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Vivien",
                    family = "Roussez",
                    role = c("aut", "cre"),
                    email = "vivien.roussez@gmail.com")
as necessary.
Packages required but not available: 'prophet', 'plotly'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) avar_mo_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Christina Harvey <harveyca@umich.edu>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'quarto'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'htmlwidgets', 'rmarkdown', 'DT'

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gergely Daroczi <daroczig@rapporter.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gergely",
                    family = "Daroczi",
                    role = c("aut", "cre"),
                    email = "daroczig@rapporter.net")
as necessary.
Packages required but not available: 'AWR', 'rJava'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gergely Daroczi <daroczig@rapporter.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gergely",
                    family = "Daroczi",
                    role = c("aut", "cre"),
                    email = "daroczig@rapporter.net")
as necessary.
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gaurav Sood <gsood07@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'lintr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Antoine Sachet <antoine.sac@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Jonathan Stott <jonathan.stott@magairports.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Simon Urbanek <simon.urbanek@R-project.org>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Simon Urbanek <simon.urbanek@R-project.org>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Antoine Sachet <antoine.sac@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Jonathan Stott <jonathan.stott@magairports.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Antoine Sachet <antoine.sac@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Antoine Sachet <antoine.sac@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'pkgdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) cosmos_mongo.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{host}{For \code{cosmos_mongo_endpoint}, the URL of the Cosmos DB MongoDB endpoint. Usually of the form "https://{account-name}.mongo.cosmos.azure.com:443/".}
       |                                                                                                                       ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rlist’

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

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'nlmixr2extra', 'nlmixr2plot', 'nlmixr2est'

Packages suggested but not available for checking:
  'lixoftConnectors', 'rmarkdown', 'spelling', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Adam B. Olshen <adam.olshen@ucsf.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Adam", "B."),
                      family = "Olshen",
                      role = c("aut", "cre"),
                      email = "adam.olshen@ucsf.edu"),
               person(given = c("Richard", "A."),
                      family = "Olshen",
                      role = "aut"),
               person(given = c("Barry", "S."),
                      family = "Taylor",
                      role = "aut"))
as necessary.
Author field differs from that derived from Authors@R
  Author:    ‘Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter), Joel Nitta [aut] (<https://orcid.org/0000-0003-4719-7472>, joelnitta)’
  Authors@R: ‘Robrecht Cannoodt [aut, cre] (ORCID: <https://orcid.org/0000-0003-3641-729X>, github: rcannood), Wouter Saelens [aut] (ORCID: <https://orcid.org/0000-0002-7114-6248>, github: zouter), Joel Nitta [aut] (ORCID: <https://orcid.org/0000-0003-4719-7472>, github: joelnitta)’
Packages required but not available: 'beastier', 'mauricer'

Packages suggested but not available for checking:
  'knitr', 'lintr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Robin K. S. Hankin <hankin.robin@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Robin", "K.", "S."),
                    family = "Hankin",
                    role = c("aut", "cre"),
                    email = "hankin.robin@gmail.com")
as necessary.
Maintainer: ‘J. Jack Lee <jjlee@mdanderson.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Nan",
                      family = "Chen",
                      role = "aut"),
               person(given = c("J.", "Jack"),
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "jjlee@mdanderson.org"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christina",
                    family = "Heinze-Deml",
                    role = c("aut", "cre"),
                    email = "heinzedeml@stat.math.ethz.ch")
as necessary.

The Description field contains
  more details, see <arXiv:1506.02494>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘dygraphs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Daniel Gerlanc <dgerlanc@enplusadvisors.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jeff",
                      family = "Enos",
                      role = "aut",
                      email = "jeff@kanecap.com"),
               person(given = "David",
                      family = "Kane",
                      role = "aut",
                      email = "dave@kanecap.com"),
               person(given = c("with", "contributions", "from", "Kyle"),
                      family = "Campbell",
                      role = "aut",
                      email = "kyle.w.campbell@williams.edu"),
               person(given = "Daniel",
                      family = "Gerlanc",
                      role = c("aut", "cre"),
                      email = "daniel@gerlanc.com"),
               person(given = "Aaron",
                      family = "Schwartz",
                      role = "aut",
                      email = "Aaron.J.Schwartz@williams.edu"),
               person(given = "Daniel",
                      family = "Suo",
                      role = "aut",
                      email = "danielsuo@gmail.com"),
               person(given = "Alexei",
                      family = "Colin",
                      role = "aut",
                      email = "acolin@fas.harvard.edu"),
               person(given = c("and", "Luyi"),
                      family = "Zhao",
                      role = "aut",
                      email = "luyizhao@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Chi Wang <chi.wang@uky.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chi",
                    family = "Wang",
                    role = c("aut", "cre"),
                    email = "chi.wang@uky.edu")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘usethis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘round_rect.r’ ‘waffle.r’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'bookdown', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rafael Santos <rafael.jpsantos@outlook.com>’

The Description field contains
  <arXiv:2001.00636>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘rlist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jiawei Zhang <zhan4362@umn.edu>’

The Description field contains
  can be found in Zhang, Ding and Yang (2021) <arXiv:1911.03063v2>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘get_cyclone.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Damien Challet <damien.challet@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Christian",
                      family = "Bongiorno",
                      role = "aut"),
               person(given = "Damien",
                      family = "Challet",
                      role = c("aut", "cre"),
                      email = "damien.challet@gmail.com"))
as necessary.

The Description field contains
  hierarchies (2020) <arXiv:2003.05807> and Ch. Bongiorno and D. Challet,
  cleaning (2020) <arXiv:2005.08703>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Caspar J van Lissa <c.j.vanlissa@tilburguniversity.edu>’

The BugReports field in DESCRIPTION has
  https://github.com/cjvanlissa/bain/
which should likely be
  https://github.com/cjvanlissa/bain/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rmarkdown’

Packages suggested but not available for checking: 'covr', 'roxygen2'

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

Packages suggested but not available for checking:
  'covr', 'DT', 'knitr', 'lintr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Hao Chen <hxchen@ucdavis.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hao",
                      family = "Chen",
                      role = c("aut", "cre"),
                      email = "hxchen@ucdavis.edu"),
               person(given = "Dylan",
                      family = "Small",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kyungtaek Park <qkrrudxor147@snu.ac.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kyungtaek",
                    family = "Park",
                    role = c("aut", "cre"),
                    email = "qkrrudxor147@snu.ac.kr")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Pawel Dlotko <pdlotko@gmail.com>’

The Description field contains
  topological data analysis" by Pawel Dlotko, (2019) <arXiv:1901.07410>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘networkD3’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘ggExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'keras', 'scoringRules', 'knitr', 'rmarkdown', 'tensorflow'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'leaflet', 'plotly'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Volker Schmid <volker.schmid@lmu.de>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Jeff Gill <jgill5402@mac.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jonathan",
                      family = "Homola",
                      role = "aut"),
               person(given = "Danielle",
                      family = "Korman",
                      role = "aut"),
               person(given = "Jacob",
                      family = "Metz",
                      role = "aut"),
               person(given = "Miguel",
                      family = "Pereira",
                      role = "aut"),
               person(given = "Mauricio",
                      family = "Vela",
                      role = "aut"),
               person(given = "Jeff",
                      family = "Gill",
                      role = c("aut", "cre"),
                      email = "jgill5402@mac.com"))
as necessary.
Package required but not available: ‘BFpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Markus Loecher <markus.loecher@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Thomas",
                      family = "Lotze",
                      role = "aut"),
               person(given = "Markus",
                      family = "Loecher",
                      role = c("aut", "cre"),
                      email = "markus.loecher@gmail.com"))
as necessary.
Package required but not available: ‘gam’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Arya Ebadi <aeba3842@uni.sydney.edu.au>’

The Description field contains
  <arXiv:2302.11837>. Such setups include target-decoy competition (TDC)
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available: 'fabR', 'madshapR'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Bill Venables <Bill.Venables@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bill",
                    family = "Venables",
                    role = c("aut", "cre"),
                    email = "Bill.Venables@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rfPermute', 'swfscMisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Eduardo Flores <eduardo@enelmargen.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Eduardo",
                    family = "Flores",
                    role = c("aut", "cre"),
                    email = "eduardo@enelmargen.org")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘dexpfit.R’ ‘expfit.R’ ‘icarfit.R’ ‘logisticfit.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Roman Hornung <hornung@ibe.med.uni-muenchen.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Roman",
                      family = "Hornung",
                      role = c("aut", "cre"),
                      email = "hornung@ibe.med.uni-muenchen.de"),
               person(given = "David",
                      family = "Causeur",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘János Hevner <hevnerjanos@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "János",
                    family = "Hevner",
                    role = c("aut", "cre"),
                    email = "hevnerjanos@hotmail.com")
as necessary.
Package required but not available: ‘DT’

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'shinytest'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) barcoding.spe.identify2.Rd:27: Lost braces; missing escapes or markup?
    27 | read.dna() from package {ape} was used to obtain DNAbin object for unaligned non-coding barcodes.
       |                         ^
Cannot process vignettes
Packages suggested but not available for checking:
  'fdm2id', 'rmarkdown', 'knitr', 'roxygen2', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kamil Erguler <k.erguler@cyi.ac.cy>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kamil",
                    family = "Erguler",
                    role = c("aut", "cre"),
                    email = "k.erguler@cyi.ac.cy")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Adam Kapelner <kapelner@qc.cuny.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Adam",
                      family = "Kapelner",
                      role = c("aut", "cre"),
                      email = "kapelner@qc.cuny.edu"),
               person(given = "Justin",
                      family = "Bleich",
                      role = "aut",
                      comment = c(ROR = "R package")),
               person(given = c("see", "COPYRIGHTS", "file", "for", "the", "authors", "of", "the", "java"),
                      family = "libraries",
                      role = "aut"))
as necessary.
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Adam Kapelner <kapelner@qc.cuny.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Adam",
                      family = "Kapelner",
                      role = c("aut", "cre"),
                      email = "kapelner@qc.cuny.edu"),
               person(given = "Justin",
                      family = "Bleich",
                      role = "aut",
                      comment = c(ROR = "R package")))
as necessary.
Packages required but not available: 'rJava', 'bartMachineJARs'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/the-BART-R-package.Rnw’
(Is a VignetteBuilder field missing?)

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

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

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'kableExtra', 'covr', 'Rraven'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Qingyan Xiang <qyxiang@bu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Qingyan",
                      family = "Xiang",
                      role = c("aut", "cre"),
                      email = "qyxiang@bu.edu"),
               person(given = "Naveen",
                      family = "Narisetty",
                      role = "aut",
                      email = "naveen@illinois.edu"))
as necessary.
Maintainer: ‘Simon Urbanek <Simon.Urbanek@r-project.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Simon",
                    family = "Urbanek",
                    role = c("aut", "cre"),
                    email = "Simon.Urbanek@r-project.org")
as necessary.
File ‘base64enc/libs/base64enc.so’:
  Found non-API call to R: ‘SETLENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘chadwick_installation.R’
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rms', 'do'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
  'listviewer', 'flextable', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'RWeka', 'rmcfs', 'rJava'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marco Vidal-Cordasco <marcovidalcordasco@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ana", "B."),
                      family = "Marín-Arroyo",
                      role = "aut"),
               person(given = "David",
                      family = "Ocio",
                      role = "aut"),
               person(given = "Marco",
                      family = "Vidal-Cordasco",
                      role = "cre",
                      email = "marcovidalcordasco@gmail.com"),
               person(given = "Delphine",
                      family = "Vettese"))
as necessary.
Maintainer: ‘Michael J. Kane <michael.kane@yale.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Author field differs from that derived from Authors@R
  Author:    ‘Lukas Baumann [aut, cre] (<https://orcid.org/0000-0001-7931-7470>), Lukas Sauer [ctb] (0000-0002-1340-9994)’
  Authors@R: ‘Lukas Baumann [aut, cre] (ORCID: <https://orcid.org/0000-0001-7931-7470>), Lukas Sauer [ctb] (ORIC: 0000-0002-1340-9994)’
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
File ‘BAS/libs/BAS.so’:
  Found non-API call to R: ‘SETLENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Mohamed", "El", "Fodil"),
                    family = "Ihaddaden",
                    role = c("aut", "cre"),
                    email = "ihaddaden.fodeil@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘John Hughes <drjphughesjr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Murali",
                      family = "Haran",
                      role = "aut",
                      email = "mharan@stat.psu.edu"),
               person(given = "John",
                      family = "Hughes",
                      role = c("aut", "cre"),
                      email = "drjphughesjr@gmail.com"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Thomas Hoffmann <tjhoffm@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Hoffmann",
                    role = c("aut", "cre"),
                    email = "tjhoffm@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Sherry Zhao<sxzhao@gwu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sherry",
                    family = "Zhao",
                    role = c("aut", "cre"),
                    email = "sxzhao@gwu.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Deepankar Basu <dbasu@umass.edu>’

The Description field contains
  to the method of Basu (2022) <arXiv:2203.12431>.  You supply the data,
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘vtable’

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Oliver Keyes <ironholds@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Oliver",
                      family = "Keyes",
                      role = c("aut", "cre"),
                      email = "ironholds@gmail.com"),
               person(given = c("Ruben", "C."),
                      family = "Arslan",
                      role = "ctb"),
               person(given = "Christopher",
                      family = "Akiki",
                      role = "ctb"),
               person(given = "Mine",
                      family = "Cetinkaya-Rundel",
                      role = "ctb"),
               person(given = "Peter",
                      family = "Meissner",
                      role = "ctb"),
               person(given = "Ilaria",
                      family = "Prosdocimi",
                      role = "ctb"),
               person(given = "Thomas",
                      family = "Leeper",
                      role = "ctb"),
               person(given = "Amy",
                      family = "Lee",
                      role = "ctb"),
               person(given = "Adolfo",
                      family = "Álvarez",
                      role = "ctb"))
as necessary.
Maintainer: ‘Chunqiao Luo <chunqiaoluo@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘polite’

Packages suggested but not available for checking:
  'Anthropometry', 'ggimage', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Evan A Martin <evanamartin@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Evan", "A"),
                      family = "Martin",
                      role = c("aut", "cre"),
                      email = "evanamartin@gmail.com"),
               person(given = c("Audrey", "Qiuyan"),
                      family = "Fu",
                      role = "aut"))
as necessary.

The Description field contains
  References: Martin and Fu (2019) <arXiv:1909.10678>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) simdata.Rd:50: height/width attributes should be in pixels
checkRd: (-1) simdata.Rd:66: height/width attributes should be in pixels
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checkRd: (-1) simdata.Rd:119: height/width attributes should be in pixels
Package required but not available: ‘ggExtra’

Package suggested but not available for checking: ‘pkgdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Riko Kelter <riko_k@gmx.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Riko",
                    family = "Kelter",
                    role = c("aut", "cre"),
                    email = "riko_k@gmx.de")
as necessary.

The Description field contains
  mixtures, see Kelter (2019) <arXiv:1906.07524>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Running examples in ‘bayesanova-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anovaplot
> ### Title: anovaplot
> ### Aliases: anovaplot
> 
> ### ** Examples
> 
> set.seed(42)
> x1=rnorm(75,0,1)
> x2=rnorm(75,1,1)
> x3=rnorm(75,2,1)
> result=bayes.anova(n=1000,first=x1,second=x2,third=x3)
Bayesian ANOVA output:
Details: Gaussian-mixture model with three components
Error in loadNamespace(x) : there is no package called ‘knitr’
Calls: bayes.anova ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Achal Lama <achal.lama@icar.gov.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Achal",
                      family = "Lama",
                      role = c("aut", "cre"),
                      email = "achal.lama@icar.gov.in"),
               person(given = c("Girish", "K"),
                      family = "Jha",
                      role = "aut"),
               person(given = c("K", "N"),
                      family = "Singh",
                      role = "aut"),
               person(given = "Bishal",
                      family = "Gurung",
                      role = "aut"))
as necessary.
Package required but not available: ‘MTS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Panagiotis Papastamoulis <papapast@yahoo.gr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Panagiotis",
                    family = "Papastamoulis",
                    role = c("aut", "cre"),
                    email = "papapast@yahoo.gr")
as necessary.
checkRd: (-1) coupledMetropolis.Rd:83-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:86-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:92-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:95-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:98-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:101-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:104-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:110-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:113-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:116-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:119-121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:122-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:125-127: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
Maintainer: ‘Li-Syuan Hong <lisyuan@nhri.org.tw>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Li-Syuan",
                    family = "Hong",
                    role = c("aut", "cre"),
                    email = "lisyuan@nhri.org.tw")
as necessary.
Unavailable namespace imported from by a ':::' call: ‘ciftiTools’
  See the note in ?`:::` about the use of this operator.
Running ‘run_BayesBrainMap_tests.R’ [0s/0s]
  Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/run_BayesBrainMap_tests.R’ failed.
Complete output:
  > # Build --> Install and Restart
  > 
  > # [Edit these]
  > ## path to your Connectome Workbench
  > my_wb <- "~/Applications/workbench"
  > ## path to test data
  > dir_data <- "tests/data"
  > ## path to results from tests
  > dir_results <- file.path(dir_data, "results")
  > 
  > library(testthat)
  > library(ciftiTools)
  Error in library(ciftiTools) : there is no package called 'ciftiTools'
  Execution halted
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Stanley E. Lazic <stan.lazic@cantab.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bruno",
                      family = "Contrino",
                      role = "aut"),
               person(given = c("Stanley", "E."),
                      family = "Lazic",
                      role = c("aut", "cre"),
                      email = "stan.lazic@cantab.net"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Specified C++11: support will be removed soon
Maintainer: ‘Aldo M. Garay <medina_garay@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Aldo", "M."),
                      family = "Garay",
                      role = c("aut", "cre"),
                      email = "medina_garay@yahoo.com"),
               person(given = c("Monique", "B."),
                      family = "Massuia",
                      role = "aut",
                      email = "moniquemassuia@gmail.com"),
               person(given = c("Victor", "H."),
                      family = "Lachos",
                      role = "aut",
                      email = "hlachos@ime.unicamp.br"),
               person(given = c("Eraldo", "B.", "Anjos"),
                      family = "Filho",
                      role = "aut",
                      email = "ebdaf1@de.ufpe.br"))
as necessary.
Maintainer: ‘Kjetil Halvorsen <kjetil1001@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Compiled", "by", "Kjetil"),
                      family = "Halvorsen",
                      role = "aut"),
               person(given = "Kjetil",
                      family = "Halvorsen",
                      role = "cre",
                      email = "kjetil1001@gmail.com"))
as necessary.
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) bayesDccGarch.Rd:91: Lost braces; missing escapes or markup?
    91 | \item{$H_n1 }{ Bayesian prediction of volatilities and co-volatilities for y_{n+1}.}
       |                                                                              ^
checkRd: (-1) bayesDccGarch.Rd:92: Lost braces; missing escapes or markup?
    92 | \item{$R_n1 }{ Bayesian prediction of coditional correlation for y_{n+1}.}
       |                                                                    ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Problems with news in ‘NEWS.md’:
No news entries found.
Maintainer: ‘Carlos Pérez <caaperezag@unal.edu.co>’

The Description field contains
  Cardona-Jiménez (2021) <arXiv:2111.01318>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) GroupSingleVoxelFETS.Rd:53: Lost braces
    53 | online trajectories related to the state parameter, the simulated BOLD responses, \mjseqn{\hat{Y}}{ascii}.
       |                                                                                                   ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Found the following HTML validation problems:
BayesDLMfMRI.html:1161:1 (GroupSingleVoxelFFBS.Rd:54): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:1287:1 (GroupSingleVoxelFSTS.Rd:54): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:1413:1 (SingleVoxelFETS.Rd:62): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:1554:1 (SingleVoxelFFBS.Rd:59): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:1690:1 (SingleVoxelFSTS.Rd:59): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:1853:1 (ffdEvidenceFETS.Rd:62): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:1994:1 (ffdEvidenceFFBS.Rd:58): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:2128:1 (ffdEvidenceFSTS.Rd:58): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:2262:1 (ffdGroupEvidenceFETS.Rd:60): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:2401:1 (ffdGroupEvidenceFFBS.Rd:56): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:2534:1 (ffdGroupEvidenceFSTS.Rd:56): Warning: <script> anchor "MathJax-script" already defined
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'tmap', 'yaml'

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'xgxr', 'projpred'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jaejoon Song <jaejoonsong@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jaejoon",
                      family = "Song",
                      role = c("aut", "cre"),
                      email = "jaejoonsong@gmail.com"),
               person(given = "Satoshi",
                      family = "Morita",
                      role = "aut"),
               person(given = c("J.", "Jack"),
                      family = "Lee",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘JuliaCall’

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

Packages suggested but not available for checking:
  'covr', 'hrf', 'INLA', 'knitr', 'rmarkdown', 'spelling'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David Ardia <david.ardia.ch@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Doug Fletcher <tug25070@temple.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Subhadeep",
                      family = "Mukhopadhyay",
                      role = "aut"),
               person(given = "Douglas",
                      family = "Fletcher",
                      role = "aut"),
               person(given = "Doug",
                      family = "Fletcher",
                      role = "cre",
                      email = "tug25070@temple.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) gMLE.bb.Rd:18: Lost braces
    18 |   \item{optim.method}{optimization method in \code{optim()}{stats}.}
       |                                                            ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘AquaticLifeHistory’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Matthew Carli <carlimm@mymail.vcu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Wheeler",
                      role = "aut"),
               person(given = "Matthew",
                      family = "Carli",
                      role = c("aut", "cre"),
                      email = "carlimm@mymail.vcu.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gordon J. Ross <gordon@gordonjross.co.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Gordon", "J."),
                    family = "Ross",
                    role = c("aut", "cre"),
                    email = "gordon@gordonjross.co.uk")
as necessary.
Specified C++11: support will be removed soon
Package required but not available: ‘xlsx’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bayeslm'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'MCPModPack', 'reactable', 'rmarkdown',
  'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) bma.bx.cy.Rd:69: Lost braces
    69 | the initial values for parameters in models. For example, inits<-function(){list(alpha=0,beta=0,c=0,var1=0.5,r=1,lamda=0.01)}.
       |                                                                            ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'heatmaply', 'networkD3', 'plotly'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Fayette Klaassen <klaassen.fayette@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Fayette",
                    family = "Klaassen",
                    role = c("aut", "cre"),
                    email = "klaassen.fayette@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'rmarkdown', 'roxygen2', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘gt’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Margarita Marin <mmarinj@unal.edu.co>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Margarita",
                      family = "Marin",
                      role = c("aut", "cre"),
                      email = "mmarinj@unal.edu.co"),
               person(given = "Edilberto",
                      family = "Cepeda-Cuervo.",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Arthur White <arwhite@tcd.ie>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jesse Windle <jesse.windle@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Problems with news in ‘NEWS.md’:
No news entries found.
Maintainer: ‘Edwin Javier Castillo Carreño <edjcastilloca@unal.edu.co>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Edwin", "Javier", "Castillo"),
                      family = "Carreño",
                      role = c("aut", "cre"),
                      email = "edjcastilloca@unal.edu.co"),
               person(given = c("Edilberto", "Cepeda"),
                      family = "Cuervo",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'flextable', 'knitr', 'rmarkdown', 'rstanarm'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tidyverse’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'covr', 'spelling', 'knitr', 'rmarkdown', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Erik Thorsén <erik.thorsen@math.su.se>’

The Description field contains
  (<arXiv:2104.02105>). The Metropolis-Hastings algorithm is designed
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Han Yu <hyu9@buffalo.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Han",
                      family = "Yu",
                      role = c("aut", "cre"),
                      email = "hyu9@buffalo.edu"),
               person(given = "Rachael",
                      family = "Blair",
                      role = "aut"),
               person(given = "Janhavi",
                      family = "Moharil",
                      role = "aut"),
               person(given = "Andrew",
                      family = "Yan",
                      role = "aut"))
as necessary.
Maintainer: ‘Daniel Turek <danielturek@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Daniel",
                      family = "Turek",
                      role = c("aut", "cre"),
                      email = "danielturek@gmail.com"),
               person(given = "Mark",
                      family = "Risser",
                      role = "aut"))
as necessary.

The Description field contains
  <arXiv:1702.00434v2>). Bayesian inference is carried out using Markov
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘helper_functions.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rstanarm', 'shinystan'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) bayesplot-package.Rd:28: height/width attributes should be in pixels
checkRd: (-1) bayesplot-package.Rd:29: height/width attributes should be in pixels
checkRd: (-1) bayesplot-package.Rd:30: height/width attributes should be in pixels
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'rstanarm'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Georg Hahn <ghahn@hsph.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Georg",
                      family = "Hahn",
                      role = c("aut", "cre"),
                      email = "ghahn@hsph.harvard.edu"),
               person(given = "Paul",
                      family = "Fearnhead",
                      role = "ctb"),
               person(given = c("Idris", "A."),
                      family = "Eckley",
                      role = "ctb"))
as necessary.
Maintainer: ‘Dries F. Benoit <Dries.Benoit@UGent.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Dries", "F."),
                      family = "Benoit",
                      role = c("aut", "cre"),
                      email = "dries.benoit@ugent.be"),
               person(given = "Rahim",
                      family = "Al-Hamzawi",
                      role = "aut"),
               person(given = "Keming",
                      family = "Yu",
                      role = "aut"),
               person(given = "Dirk",
                      family = "Van den Poel",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'scoringRules'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Specified C++11: support will be removed soon
Packages required but not available: 'colourpicker', 'config', 'golem'

Package suggested but not available for checking: ‘spelling’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Minsuk Shin <minsuk000@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Minsuk",
                      family = "Shin",
                      role = c("aut", "cre"),
                      email = "minsuk000@gmail.com"),
               person(given = "Ruoxuan",
                      family = "Tian",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jinhui Yang <james.yangjinhui@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jinhui",
                      family = "Yang",
                      role = c("aut", "cre"),
                      email = "james.yangjinhui@gmail.com"),
               person(given = "Haitao",
                      family = "Chu",
                      role = "aut"),
               person(given = "Lifeng",
                      family = "Lin",
                      role = "aut"))
as necessary.
Maintainer: ‘Jean-Michel Marin <jean-michel.marin@umontpellier.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jean-Michel",
                      family = "Marin",
                      role = c("aut", "cre"),
                      email = "jean-michel.marin@umontpellier.fr"),
               person(given = c("Christian", "P."),
                      family = "Robert",
                      role = "aut"))
as necessary.
'library' or 'require' call not declared from: ‘mvtnorm’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Maintainer: ‘Stephanie van der Pas <s.l.vanderpas@amsterdamumc.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Stephanie",
                      family = "van der Pas",
                      role = c("aut", "cre"),
                      email = "s.l.vanderpas@amsterdamumc.nl"),
               person(given = "Ismael",
                      family = "Castillo",
                      role = "aut"))
as necessary.

The Description field contains
  <arXiv:2005.02889>. In that paper it is also shown that the credible
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘riskRegression’

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'mediation', 'rmarkdown', 'rstanarm'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Riko Kelter <riko.kelter@uni-siegen.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Riko",
                    family = "Kelter",
                    role = c("aut", "cre"),
                    email = "riko.kelter@uni-siegen.de")
as necessary.

The Description field contains
  details about the Gibbs sampler see Kelter (2019) <arXiv:1906.07524>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexia",
                    family = "Jolicoeur-Martineau",
                    role = c("aut", "cre"),
                    email = "alexia.jolicoeur-martineau@mail.mcgill.ca")
as necessary.
checkRd: (-1) BayesTreePrior.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:41: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Robert McCulloch <robert.e.mcculloch@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hugh",
                      family = "Chipman",
                      role = "aut",
                      email = "hugh.chipman@gmail.com"),
               person(given = "Robert",
                      family = "McCulloch",
                      role = c("aut", "cre"),
                      email = "robert.e.mcculloch@gmail.com"))
as necessary.
Maintainer: ‘Inga Schwabe <bayestwin@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Inga",
                    family = "Schwabe",
                    role = c("aut", "cre"),
                    email = "bayestwin@gmail.com")
as necessary.

The BugReports field in DESCRIPTION has
  https://github.com/ingaschwabe/BayesTwin
which should likely be
  https://github.com/ingaschwabe/BayesTwin/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘yaml’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Edward M.H. Lin <ed.mhlin@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Cathy", "W.", "S."),
                      family = "Chen",
                      role = "aut"),
               person(given = c("Edward", "M.H."),
                      family = "Lin",
                      role = c("aut", "cre"),
                      email = "ed.mhlin@gmail.com"),
               person(given = "F.C.",
                      family = "Liu",
                      role = "aut"),
               person(given = "Richard",
                      family = "Gerlach",
                      role = "aut"))
as necessary.
Maintainer: ‘Erik W Leppo <Erik.Leppo@tetratech.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rebecca",
                      family = "Murphy",
                      role = "aut"),
               person(given = "Elgin",
                      family = "Perry",
                      role = "aut"),
               person(given = "Jennifer",
                      family = "Keisman",
                      role = "aut"),
               person(given = "Jon",
                      family = "Harcum",
                      role = "aut"),
               person(given = c("Erik", "W"),
                      family = "Leppo",
                      role = c("aut", "cre"),
                      email = "erik.leppo@tetratech.com"))
as necessary.
Package required but not available: ‘knitr’

Packages suggested but not available for checking: 'devtools', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Valeriy Zakamulin <valeriz@uia.no>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Valeriy",
                    family = "Zakamulin",
                    role = c("aut", "cre"),
                    email = "valeriz@uia.no")
as necessary.
Maintainer: ‘Anton Gagin <av.gagin@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Anton",
                      family = "Gagin",
                      role = c("aut", "cre"),
                      email = "av.gagin@gmail.com"),
               person(given = c("Igor", "Levin", "with", "contributions", "from", "Charles", "R.", "Hogg"),
                      family = "III",
                      role = "aut"))
as necessary.
checkRd: (-1) runUI.Rd:11: Lost braces
    11 | Runs a \bold{Shiny} application. This function normally does not return; interrupt bold{R} to stop the application (usually by pressing Ctrl+C or Esc).
       |                                                                                        ^
Package required but not available: ‘Seurat’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

Package in Depends/Imports which should probably only be in LinkingTo: ‘RcppEigen’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) getOperatingSystem.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:30: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages suggested but not available for checking: 'rms', 'Hmisc', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/mle2.Rnw’
   ‘inst/doc/quasi.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Paul Gilbert <pgilbert.ttv9z@ncf.ca>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Note: skipping ‘BBvignetteJSS.Stex’ due to unavailable dependencies:
  'Hmisc'
Maintainer: ‘Vinicius Mayrink <vdinizm@gmail.com>’

The Description field contains
  <arXiv:2003.05157>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘boot_bw.R’ ‘boot_bw_estimate.R’ ‘post_strat_estimation.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Wang Yudong <yudongw@u.nus.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wang",
                      family = "Yudong",
                      role = c("aut", "cre"),
                      email = "yudongw@u.nus.edu"),
               person(given = "Ye",
                      family = "Zhisheng",
                      role = "aut"),
               person(given = "Cao",
                      family = "Hongyuan",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Longhai Li <longhai@math.usask.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Longhai",
                    family = "Li",
                    role = c("aut", "cre"),
                    email = "longhai@math.usask.ca")
as necessary.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
Maintainer: ‘Haoran Zhang <hzz0017@auburn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Haoran",
                    family = "Zhang",
                    role = c("aut", "cre"),
                    email = "hzz0017@auburn.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'survminer'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mahdi Teimouri <teimouri@aut.ac.ir>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mahdi",
                    family = "Teimouri",
                    role = c("aut", "cre"),
                    email = "teimouri@aut.ac.ir")
as necessary.
checkRd: (-1) goftype1.Rd:4: Lost braces
     4 | \description{The goodness-of-fit (GOF) measures consist of Anderson-Darling (\code{AD}) and Cram\'{e}er-von Misses (\code{CVM}) statistics for progressive type-I interval censoring scheme are given, respectively, by
       |                                                                                                   ^
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'leaflet', 'leaflet.extras'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ewoud De Troyer <ewoud.detroyer@uhasselt.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Aregay",
                      family = "Mengsteab",
                      role = "aut"),
               person(given = "Martin",
                      family = "Otava",
                      role = "aut"),
               person(given = "Tatsiana",
                      family = "Khamiakova",
                      role = "aut"),
               person(given = "Ewoud",
                      family = "De Troyer",
                      role = c("aut", "cre"),
                      email = "ewoud.detroyer@uhasselt.be"))
as necessary.
Found the following files/directories:
  ‘fabiabreast.txt’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Denis Talbot <denis.talbot@fmed.ulaval.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Denis",
                      family = "Talbot",
                      role = c("aut", "cre"),
                      email = "denis.talbot@fmed.ulaval.ca"),
               person(given = "Genevieve",
                      family = "Lefebvre",
                      role = "aut"),
               person(given = "Juli",
                      family = "Atherton",
                      role = "aut"),
               person(given = "Yohann",
                      family = "Chiu.",
                      role = "aut"))
as necessary.
Maintainer: ‘Jared S. Murray <jared.murray@mccombs.utexas.edu>’

The Description field contains
  <arXiv:1309.1906>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Nicola Lunardon <nicola.lunardon@unimib.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Nicola",
                      family = "Lunardon",
                      role = c("aut", "cre"),
                      email = "nicola.lunardon@unimib.it"),
               person(given = "Daniel",
                      family = "Scharfstein",
                      role = "aut",
                      email = "dscharf@jhu.edu"))
as necessary.
Maintainer: ‘J. Jack Lee <jjlee@mdanderson.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Nan",
                      family = "Chen",
                      role = "aut"),
               person(given = c("J.", "Jack"),
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "jjlee@mdanderson.org"))
as necessary.
Package required but not available: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jiehuan Sun <jiehuan.sun@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jiehuan",
                      family = "Sun",
                      role = c("aut", "cre"),
                      email = "jiehuan.sun@gmail.com"),
               person(given = c("Jose", "D."),
                      family = "Herazo-Maya",
                      role = "aut"),
               person(given = "Naftali",
                      family = "Kaminski",
                      role = "aut"),
               person(given = "Hongyu",
                      family = "Zhao",
                      role = "aut"),
               person(given = c("Joshua", "L."),
                      family = "Warren,",
                      role = "aut"))
as necessary.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘bcdata’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Eliezer Gurarie <egurarie@esf.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Eliezer",
                    family = "Gurarie",
                    role = c("aut", "cre"),
                    email = "egurarie@esf.edu")
as necessary.
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/bcpa.rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Fanni Zhang <rstatpackages@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Fanni",
                    family = "Zhang",
                    role = c("aut", "cre"),
                    email = "rstatpackages@gmail.com")
as necessary.
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘BRugs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Duc-Khanh To  <toduc@stat.unipd.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Duc-Khanh",
                      family = "To",
                      role = c("aut", "cre"),
                      email = "toduc@stat.unipd.it"),
               person(given = c("with", "contributions", "from", "Monica"),
                      family = "Chiogna",
                      role = "aut"),
               person(given = "Gianfranco",
                      family = "Adimari",
                      role = "aut"))
as necessary.
Package required but not available: ‘rgl’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘spelling.R’ [0s/0s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Maintainer: ‘Valentinian Mihai Lungu <valentinian.mihai@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ioannis",
                      family = "Papageorgiou",
                      role = "aut"),
               person(given = c("Valentinian", "Mihai"),
                      family = "Lungu",
                      role = c("aut", "cre"),
                      email = "valentinian.mihai@gmail.com"),
               person(given = "Ioannis",
                      family = "Kontoyiannis",
                      role = "aut"))
as necessary.

The Description field contains
  April 2022. Available at: <arXiv:2007.14900> [stat.ME], July 2020] and
  using Bayesian Context Trees' <arXiv:2203.04341> [stat.ME], March
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BCT.Rcheck/00install.out’ for details.
Maintainer: ‘Michal Burdukiewicz <michalburdukiewicz@gmail.com>’

The Description field contains
  article (at <arXiv:0908.2062>) and Perry's 2009 PhD thesis (at
  <arXiv:0909.3052>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘DT’

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Guzman Santafe <guzman.santafe@unavarra.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Guzman",
                      family = "Santafe",
                      role = c("aut", "cre"),
                      email = "guzman.santafe@unavarra.es"),
               person(given = "Borja",
                      family = "Calvo",
                      role = "aut"),
               person(given = "Aritz",
                      family = "Perez",
                      role = "aut"),
               person(given = c("Jose", "A."),
                      family = "Lozano",
                      role = "aut"))
as necessary.
checkRd: (-1) bde.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:56: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking:
  'skimr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Manuel Wiesenfarth <m.wiesenfarth@dkfz.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Annette",
                      family = "Kopp-Schneider",
                      role = "aut"),
               person(given = "Manuel",
                      family = "Wiesenfarth",
                      role = c("aut", "cre"),
                      email = "m.wiesenfarth@dkfz.de"),
               person(given = "Ulrich",
                      family = "Abel",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘rmarkdown’

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Solvi Rognvaldsson <solviro@gmail.com>’

The Description field contains
  described in Hrafnkelsson et al. (2020) <arXiv:2010.04769>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(vdiffr)
  > library(covr)
  Error in library(covr) : there is no package called 'covr'
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Found the following files/directories:
  ‘dump.txt’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Terry Therneau <therneau.terry@mayo.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Terry",
                    family = "Therneau",
                    role = c("aut", "cre"),
                    email = "therneau.terry@mayo.edu")
as necessary.
Package required but not available: ‘knitr’

Packages suggested but not available for checking: 'rmarkdown', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Hamed Haselimashhadi <hamedhaseli@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hamed",
                    family = "Haselimashhadi",
                    role = c("aut", "cre"),
                    email = "hamedhaseli@gmail.com")
as necessary.
Packages required but not available: 'DT', 'rJava', 'devtools'

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

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Peter Kampstra <beanplot@kampstra.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Peter",
                    family = "Kampstra",
                    role = c("aut", "cre"),
                    email = "beanplot@kampstra.net")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Chenguang Wang <cwang68@jhmi.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chenguang",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "cwang68@jhmi.edu"),
               person(given = "Ravi",
                      family = "Varadhan",
                      role = "aut"),
               person(given = c("Trustees", "of", "Columbia"),
                      family = "University",
                      role = "cph",
                      comment = "tools/make_cpp.R, R/stanmodels.R"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DT'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'DT', 'htmlwidgets', 'yaml'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Panagiotis Papastamoulis <papapast@yahoo.gr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Panagiotis",
                    family = "Papastamoulis",
                    role = c("aut", "cre"),
                    email = "papapast@yahoo.gr")
as necessary.

The Description field contains
  Papastamoulis et al (2017) <arXiv:1709.06111> for a detailed
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Package required but not available: ‘mixtools’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gideon Bradburd <bradburd@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gideon",
                    family = "Bradburd",
                    role = c("aut", "cre"),
                    email = "bradburd@umich.edu")
as necessary.
Packages required but not available: 'visNetwork', 'DT'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'RobinCar'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘apply_contrast.R’ ‘apply_contrast.Rd’ ‘average_predictions.Rd’
    ‘estimate_varcov.R’ ‘estimate_varcov.Rd’ ‘get_marginal_effect.R’
    ‘get_marginal_effect.Rd’ ‘predict_counterfactuals.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'tidyverse', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘fitting.R’
Maintainer: ‘Peter Thuresson <jpeter.thuresson@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Peter",
                    family = "Thuresson",
                    role = c("aut", "cre"),
                    email = "jpeter.thuresson@gmail.com")
as necessary.
Packages required but not available:
  'DiagrammeR', 'knitr', 'rmdpartials', 'ufs', 'yum'

Packages suggested but not available for checking:
  'kableExtra', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jakub Nowosad <nowosad.jakub@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running examples in ‘benchmarkmeData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_datatable_past
> ### Title: Interactive table of results
> ### Aliases: get_datatable_past
> 
> ### ** Examples
> 
> ## Need the DT package
> ## View all results for prog test
> get_datatable_past("prog")
Error: Install DT package to use datatable
Execution halted
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'DT', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Valentin Thorey <valentin@dreem.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dylan",
                      family = "Heirstraeten",
                      role = "aut"),
               person(given = "Valentin",
                      family = "Thorey",
                      role = "cre",
                      email = "valentin@dreem.com"))
as necessary.
Maintainer: ‘Carlos Cinelli <carloscinelli@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Carlos",
                    family = "Cinelli",
                    role = c("aut", "cre"),
                    email = "carloscinelli@hotmail.com")
as necessary.
Maintainer: ‘Vitor Hugo Moreau <vitorhmc@ufba.br>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Vitor", "Hugo"),
                    family = "Moreau",
                    role = c("aut", "cre"),
                    email = "vitorhmc@ufba.br")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Grace Chiu <bentcable@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Grace",
                      family = "Chiu",
                      role = c("aut", "cre"),
                      email = "bentcable@gmail.com"),
               person(given = c("Virginia", "Institute", "of", "Marine"),
                      family = "Science",
                      role = "aut"),
               person(given = c("William", "&", "Mary", "PO", "Box"),
                      family = "1346",
                      role = "aut"),
               person(given = "Gloucester",
                      family = "Point",
                      role = "aut"),
               person(given = "VA",
                      family = "23062",
                      role = "aut"),
               person(family = "USA",
                      role = "aut"))
as necessary.
checkRd: (-1) sockeye.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sockeye.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:14: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kyun-Seop Bae <k@acr.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kyun-Seop",
                    family = "Bae",
                    role = c("aut", "cre"),
                    email = "k@acr.kr")
as necessary.
Maintainer: ‘Alberto Caimo <alberto.caimo1@ucd.ie>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alberto",
                      family = "Caimo",
                      role = c("aut", "cre"),
                      email = "alberto.caimo1@ucd.ie"),
               person(given = "Lampros",
                      family = "Bouranis",
                      role = "aut"),
               person(given = "Robert",
                      family = "Krause",
                      role = "ctb"))
as necessary.
Package required but not available: ‘ergm’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Cannot process vignettes
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  'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
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  'knitr', 'rmarkdown', 'leaflet', 'leaflet.extras'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yuanhao Lai <ylai72@uwo.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "A.I.",
                      family = "McLeod",
                      role = "aut"),
               person(given = "Changjiang",
                      family = "Xu",
                      role = "aut"),
               person(given = "Yuanhao",
                      family = "Lai",
                      role = c("aut", "cre"),
                      email = "ylai72@uwo.ca"))
as necessary.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jack Kuipers <jack.kuipers@bsse.ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jack",
                      family = "Kuipers",
                      role = c("aut", "cre"),
                      email = "jack.kuipers@bsse.ethz.ch"),
               person(given = "Giusi",
                      family = "Moffa",
                      role = "aut"))
as necessary.
Cannot process vignettes
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  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Beaulac Cedric <cedric@utstat.toronto.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Description field contains
  Rosentahl (2019) <arXiv:1804.10168>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
checkRd: (-1) gen.data.Rd:42: Lost braces
    42 | code{cortype = 2} denotes the constant structure, where the \eqn{(i,j)} entry of covariance
       |     ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rlist', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Haiming Zhou <haiming2019@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Telmo M Silva Filho <tmfilho@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Telmo", "M", "Silva"),
                      family = "Filho",
                      role = c("aut", "cre"),
                      email = "tmfilho@gmail.com"),
               person(given = "Meelis",
                      family = "Kull",
                      role = "aut"))
as necessary.
Package required but not available: ‘plotly’

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VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Haakon Eidem Haakstad <h.e.haakstad@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Haakon", "Eidem"),
                    family = "Haakstad",
                    role = c("aut", "cre"),
                    email = "h.e.haakstad@gmail.com")
as necessary.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'quarto'

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michele De Meo <micheledemeo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michele",
                    family = "De Meo",
                    role = c("aut", "cre"),
                    email = "micheledemeo@gmail.com")
as necessary.
Malformed Title field: should not end in a period.
Maintainer: ‘Qingyuan Zhao <qyzhao@statslab.cam.ac.uk>’

The Description field contains
  <arXiv:2004.07743>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available:
  'plotly', 'rmarkdown', 'dygraphs', 'DT'

Packages suggested but not available for checking: 'devtools', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Chris Aberson <cla18@humboldt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chris",
                    family = "Aberson",
                    role = c("aut", "cre"),
                    email = "cla18@humboldt.edu")
as necessary.
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/Guide.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Blondeau Da Silva Stephane <Stephane.Blondeau-Da-Silva@ac-limoges.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Blondeau", "Da", "Silva"),
                    family = "Stephane",
                    role = c("aut", "cre"),
                    email = "stephane.blondeau-da-silva@ac-limoges.fr")
as necessary.
Maintainer: ‘Aaron Olsen <aarolsen@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Aaron",
                    family = "Olsen",
                    role = c("aut", "cre"),
                    email = "aarolsen@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2', 'devtools', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'ergm', 'Bergm'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'roxygen2', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/using-bfpwr.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Giampiero Marra <giampiero.marra@ucl.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Giampiero",
                      family = "Marra",
                      role = c("aut", "cre"),
                      email = "giampiero.marra@ucl.ac.uk"),
               person(given = "Raffaella",
                      family = "Calabrese",
                      role = "aut"),
               person(given = c("Silvia", "Angela"),
                      family = "Osmetti",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘BFpack’

Packages suggested but not available for checking:
  'networktools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'ggpedigree', 'kinship2', 'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Przemyslaw Biecek <Przemyslaw.Biecek@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Przemyslaw", "Biecek", "\\&", "Ewa"),
                      family = "Szczurek",
                      role = "aut"),
               person(given = "Przemyslaw",
                      family = "Biecek",
                      role = "cre",
                      email = "Przemyslaw.Biecek@gmail.com"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'qgraph', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Emilio Akira Morones Ishikawa <emiliomorones@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("L.", "E."),
                      family = "Nieto-Barajas",
                      role = "aut"),
               person(given = c("J.", "A.", "Garcia"),
                      family = "Bueno",
                      role = "aut"),
               person(given = c("E.A.", "Morones"),
                      family = "Ishikawa",
                      role = "aut"),
               person(given = "J.",
                      family = "Pliego",
                      role = "aut"),
               person(given = c("Emilio", "Akira", "Morones"),
                      family = "Ishikawa",
                      role = "cre",
                      email = "emiliomorones@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yin Song <yinsong@uvic.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yin",
                      family = "Song",
                      role = c("aut", "cre"),
                      email = "yinsong@uvic.ca"),
               person(given = "Shufei",
                      family = "Ge",
                      role = "aut"),
               person(given = "Liangliang",
                      family = "Wang",
                      role = "aut"),
               person(given = "Jiguo",
                      family = "Cao",
                      role = "aut"),
               person(given = "Keelin",
                      family = "Greenlaw",
                      role = "aut"),
               person(given = "Mary",
                      family = "Lesperance",
                      role = "aut"),
               person(given = c("Farouk", "S."),
                      family = "Nathoo",
                      role = "aut"))
as necessary.
checkRd: (-1) sp_bgsmtr.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{c.star}{The threshold for computing posterior tail probabilities p_{ij} for Bayesian FDR as defined in Section 3.2 of  Song, Ge et al.(2019). If not specified the default is to set this threshold as the minimum posterior standard deviation, where the minimum is taken over all regression coefficients in the model.}
       |                                                                          ^
Author field differs from that derived from Authors@R
  Author:    ‘Pedro C. Brom [aut, cre, cph] (<https://orcid.org/0000-0002-1288-7695>, http://lattes.cnpq.br/0154064396756002), Cira E. G. Otiniano [aut, cph] (<https://orcid.org/0000-0002-5619-0478>, http://lattes.cnpq.br/0307717595727716), Roberto Vila [aut, cph] (<https://orcid.org/0000-0003-1073-0114>, http://lattes.cnpq.br/4978745622057574), Marcelo B. Pereira [aut, cph] (<https://orcid.org/0000-0002-1182-5193>, https://lattes.cnpq.br/9358366674842900)’
  Authors@R: ‘Pedro C. Brom [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-1288-7695>, Lattes: http://lattes.cnpq.br/0154064396756002), Cira E. G. Otiniano [aut, cph] (ORCID: <https://orcid.org/0000-0002-5619-0478>, Lattes: http://lattes.cnpq.br/0307717595727716), Roberto Vila [aut, cph] (ORCID: <https://orcid.org/0000-0003-1073-0114>, Lattes: http://lattes.cnpq.br/4978745622057574), Marcelo B. Pereira [aut, cph] (ORCID: <https://orcid.org/0000-0002-1182-5193>, Lattes: https://lattes.cnpq.br/9358366674842900)’
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kjetil B.Halvorsen <kjetil1001@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ernesto",
                      family = "Barrios",
                      role = "aut"),
               person(given = "Kjetil",
                      family = "B.Halvorsen",
                      role = "cre",
                      email = "kjetil1001@gmail.com"))
as necessary.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Maintainer: ‘Stephan Wojciekowski <stephan.wojciekowski@boehringer-ingelheim.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘DT’

Package suggested but not available for checking: ‘lintr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Agner Fog <agner@agner.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Agner",
                    family = "Fog",
                    role = c("aut", "cre"),
                    email = "agner@agner.org")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘De Troyer Ewoud <ewoud.detroyer@uhasselt.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("De", "Troyer"),
                    family = "Ewoud",
                    role = c("aut", "cre"),
                    email = "ewoud.detroyer@uhasselt.be")
as necessary.
Packages required but not available:
  'contentanalysis', 'DT', 'plotly', 'visNetwork'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'wordcloud2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Aurélien Goutsmedt <agoutsmedt@hotmail.fr>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rcrossref', 'yamlme'

Packages suggested but not available for checking:
  'covr', 'devtools', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mahdi Teimouri <teimouri@aut.ac.ir>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mahdi",
                    family = "Teimouri",
                    role = c("aut", "cre"),
                    email = "teimouri@aut.ac.ir")
as necessary.
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Alexander F. Lapanowski <aflapan@gmail.com>’

The Description field contains
  <arXiv:2005.03858>.  Also includes methods for non-linear discriminant
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Sebastian Kaiser <dr.sebastian.kaiser@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sebastian",
                      family = "Kaiser",
                      role = c("aut", "cre"),
                      email = "dr.sebastian.kaiser@gmail.com"),
               person(given = "Rodrigo",
                      family = "Santamaria",
                      role = "aut"),
               person(given = "Tatsiana",
                      family = "Khamiakova",
                      role = "aut"),
               person(given = "Martin",
                      family = "Sill",
                      role = "aut"),
               person(given = "Roberto",
                      family = "Theron",
                      role = "aut"),
               person(given = "Luis",
                      family = "Quintales",
                      role = "aut"),
               person(given = "Friedrich",
                      family = "Leisch",
                      role = "aut"),
               person(given = "Ewoud",
                      family = "De Troyer",
                      role = "aut"),
               person(given = "Sami",
                      family = "Leon.",
                      role = "aut"))
as necessary.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  diagnosticTest.Rd: additivityTests
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Polina Suter <polina.suter@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Polina",
                      family = "Suter",
                      role = c("aut", "cre"),
                      email = "polina.suter@gmail.com"),
               person(given = "Jack",
                      family = "Kuipers",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) BiDimRegression.Rd:29: Lost braces; missing escapes or markup?
    29 | \item \code{euclidean.df1, affine.df1} -  degrees of freedom of the nominator used for the F-statistics propagated by Nakaya (1997); df1 = p-2, with p is the number of elements  needed to calculate the referring model: p=4 for the Euclidean and p=6 for the affine geometry {Nakaya, 1997, Table 1}.
       |                                                                                                                                                                                                                                                                                  ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'DiagrammeR', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(family = "BIFIE",
                      role = "aut"),
               person(given = "Alexander",
                      family = "Robitzsch",
                      role = c("aut", "cre"),
                      email = "robitzsch@ipn.uni-kiel.de"),
               person(given = "Konrad",
                      family = "Oberwimmer",
                      role = "aut"))
as necessary.
Package required but not available: ‘fMultivar’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gabriel Martos <gmartos@utdt.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘entropy.fd.Rd’:
    \keyword{rkhs, Entropy}
Cannot process vignettes
Packages suggested but not available for checking:
  'BiocStyle', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Steve Mack <Steven.Mack@ucsf.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Derek",
                      family = "Pappas",
                      role = "aut",
                      email = "djpappas75@gmail.com"),
               person(given = "Steve",
                      family = "Mack",
                      role = c("aut", "cre"),
                      email = "Steven.Mack@ucsf.edu"),
               person(given = "Jill",
                      family = "Hollenbach",
                      role = "aut",
                      email = "Jill.Hollenbach@ucsf.edu"))
as necessary.
Package required but not available: ‘haplo.stats’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'bookdown', 'INLA', 'knitr', 'rmarkdown', 'tmap'

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

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Thomas Lumley <t.lumley@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Lumley",
                    role = c("aut", "cre"),
                    email = "t.lumley@auckland.ac.nz")
as necessary.
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
Packages required but not available: 'plotly', 'htmlwidgets'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DT'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Joan Garriga <jgarriga@ceab.csic.es>’

The Description field contains
  F. (2018), <arXiv:1812.09869>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++14: support will be removed soon
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                         ^
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                                                                                   ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ruoqi Yu <ruoqiyu125@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ruoqi",
                    family = "Yu",
                    role = c("aut", "cre"),
                    email = "ruoqiyu125@gmail.com")
as necessary.
Maintainer: ‘Cristian Pachón García <cc.pachon@gmail.com>’

The Description field contains
  proposed by Delicado P. and C. Pachón-García (2021) <arXiv:2007.11919>
  (2021) <arXiv:2007.11919> (original proposal).  - Fast MDS, proposed by
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rms', 'sgPLS', 'survAUC'

Packages suggested but not available for checking:
  'knitr', 'plsRcox', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Thomas Lumley <t.lumley@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Lumley",
                    role = c("aut", "cre"),
                    email = "t.lumley@auckland.ac.nz")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) pQF.Rd:30: Lost braces; missing escapes or markup?
    30 | When \code{M} is not square, a randomised estimator for the trace of \code{crossprod(M)^2} is used. This is the sample size. When \code{M} is of \code{"matrixfree"} and does not include the trace of {crossprod(M)} as a component, this sample size will also be used to compute that. See Hutchinson reference. }
       |                                                                                                                                                                                                        ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Maintainer: ‘Chibisi Chima-Okereke <chibisi@active-analytics.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chibisi",
                    family = "Chima-Okereke",
                    role = c("aut", "cre"),
                    email = "chibisi@active-analytics.com")
as necessary.
Package required but not available: ‘JuliaCall’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [161s/196s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Maintainer: ‘Nathaniel E. Helwig <helwig@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Nathaniel", "E."),
                    family = "Helwig",
                    role = c("aut", "cre"),
                    email = "helwig@umn.edu")
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘bigsplines-package.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘bigssa.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘bigssg.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘bigssp.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘bigtps.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘makessa.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘makessg.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘makessp.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘ordspline.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘predict.bigspline.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘predict.bigssa.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘predict.bigssg.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘predict.bigssp.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘predict.bigtps.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘predict.ordspline.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
  File ‘ssBasis.Rd’:
    http://dx.doi.org/10.3389/fams.2017.00015
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [71s/86s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Aliasghar Tarkhan <atarkhan@uw.edu>’

The Description field contains
  <arXiv:2003.00116v2>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Michael J. Kane <bigmemoryauthors@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Michael", "J."),
                      family = "Kane",
                      role = c("aut", "cre"),
                      email = "kaneplusplus@gmail.com"),
               person(given = c("John", "W."),
                      family = "Emerson",
                      role = "aut",
                      email = "jayemerson@gmail.com"))
as necessary.
Maintainer: ‘Chenguang Wang <cwang68@jhmi.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chenguang",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "cwang68@jhmi.edu"),
               person(given = "Chiung-Yu",
                      family = "Huang",
                      role = "aut"),
               person(given = "Mei-Cheng",
                      family = "Wang",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘M. Helena Goncalves <mhgoncal@ualg.pt>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("M.", "Helena"),
                      family = "Goncalves",
                      role = c("aut", "cre"),
                      email = "mhgoncal@ualg.pt"),
               person(given = c("M.", "Salome"),
                      family = "Cabral",
                      role = "aut"),
               person(given = "Adelchi",
                      family = "Azzalini",
                      role = "aut"),
               person(given = c("apart", "from", "a", "set", "of", "Fortran-77", "subroutines", "written", "by", "R."),
                      family = "Piessens",
                      role = "aut"),
               person(given = "E.",
                      family = "de Doncker",
                      role = "aut"),
               person(given = c("belonging", "to", "the", "suite"),
                      family = "\"Quadpack\".",
                      role = "aut"))
as necessary.
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mikkel Freltoft Krogsholm <mikkel@56n.dk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Mikkel", "Freltoft"),
                    family = "Krogsholm",
                    role = c("aut", "cre"),
                    email = "mikkel@56n.dk")
as necessary.
Maintainer: ‘Navinkumar Nedunchezhian <navinkumar.nedunchezhian@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Navinkumar",
                    family = "Nedunchezhian",
                    role = c("aut", "cre"),
                    email = "navinkumar.nedunchezhian@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Chih-Li Sung <iamdfchile@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chih-Li",
                    family = "Sung",
                    role = c("aut", "cre"),
                    email = "iamdfchile@gmail.com")
as necessary.

The Description field contains
  can be seen in Sung et al (2017) <arXiv:1705.02511>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Dirk Eddelbuettel <edd@debian.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dirk",
                      family = "Eddelbuettel",
                      role = c("aut", "cre"),
                      email = "edd@debian.org"),
               person(given = "Ista",
                      family = "Zahn",
                      role = "aut"),
               person(given = "Rob",
                      family = "Hyndman",
                      role = "aut"))
as necessary.
Packages required but not available: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Josué M. Polanco-Martínez <josue.m.polanco@gmail.com>’

Found the following (possibly) invalid file URIs:
  URI: josue.m.polanco@gmail.com
    From: man/BINCOR-package.Rd
  URI: josue.m.polanco@gmail.com
    From: man/bin_cor.Rd
  URI: josue.m.polanco@gmail.com
    From: man/ccf_ts.Rd
  URI: josue.m.polanco@gmail.com
    From: man/cor_ts.Rd
  URI: josue.m.polanco@gmail.com
    From: man/plot_ts.Rd
  URI: mvkorpel@iki.fi
    From: man/redfitMinls.Rd
  URI: mvkorpel@iki.fi
    From: man/redfitTauest.Rd
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
Maintainer: ‘Korbinian Strimmer <strimmerlab@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sebastian",
                      family = "Gibb",
                      role = "aut"),
               person(given = "Korbinian",
                      family = "Strimmer.",
                      role = "aut"),
               person(given = "Korbinian",
                      family = "Strimmer",
                      role = "cre",
                      email = "strimmerlab@gmail.com"))
as necessary.
Maintainer: ‘Samuel V. Scarpino <s.scarpino@northeastern.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Samuel", "V."),
                      family = "Scarpino",
                      role = c("aut", "cre"),
                      email = "s.scarpino@northeastern.edu"),
               person(given = "Paul",
                      family = "von Hippel",
                      role = "aut"),
               person(given = "Igor",
                      family = "Holas",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following (possibly) invalid file URI:
  URI: doi.org/10.1177/0081175015599807
    From: inst/CITATION
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Berkley Shands <rpackages@biorankings.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Terrence",
                      family = "Brooks",
                      role = "aut"),
               person(given = "Berkley",
                      family = "Shands",
                      role = c("aut", "cre"),
                      email = "rpackages@biorankings.com"),
               person(given = "Skye",
                      family = "Buckner-Petty",
                      role = "aut"),
               person(given = c("Patricio", "S."),
                      family = "La Rosa",
                      role = "aut"),
               person(given = "Elena",
                      family = "Deych",
                      role = "aut"),
               person(given = c("William", "D."),
                      family = "Shannon",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Matt Nunes <nunesrpackages@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Matt",
                    family = "Nunes",
                    role = c("aut", "cre"),
                    email = "nunesrpackages@gmail.com")
as necessary.
Package required but not available: ‘yaml’

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Frank Schaarschmidt <schaarschmidt@biostat.uni-hannover.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Frank",
                    family = "Schaarschmidt",
                    role = c("aut", "cre"),
                    email = "schaarschmidt@biostat.uni-hannover.de")
as necessary.
Maintainer: ‘Ran Gao <rgao8@uic.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gul",
                      family = "Inan",
                      role = "aut"),
               person(given = "Hakan",
                      family = "Demirtas",
                      role = "aut"),
               person(given = "Ran",
                      family = "Gao",
                      role = c("aut", "cre"),
                      email = "rgao8@uic.edu"))
as necessary.
Package required but not available: ‘rlist’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sundar Dorai-Raj <sdorairaj@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sundar",
                    family = "Dorai-Raj",
                    role = c("aut", "cre"),
                    email = "sundar.dorai-raj@pdf.com")
as necessary.
checkRd: (-1) binom.confint.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:32-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:45: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Ran Gao <rgao8@uic.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hakan",
                      family = "Demirtas",
                      role = "aut"),
               person(given = "Yue",
                      family = "Wang",
                      role = "aut"),
               person(given = "Rawan",
                      family = "Allozi",
                      role = "aut"),
               person(given = "Ran",
                      family = "Gao",
                      role = c("aut", "cre"),
                      email = "rgao8@uic.edu"))
as necessary.
Maintainer: ‘Ping Liu <ping.liu@unimelb.edu.au>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Sergei Izrailev <sizrailev@jabiruventures.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sergei",
                    family = "Izrailev",
                    role = c("aut", "cre"),
                    email = "sizrailev@jabiruventures.com")
as necessary.
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/BinSegBstrap.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'covr', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael P. Fay <mfay@niaid.nih.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jenn",
                      family = "Kirk",
                      role = "aut"),
               person(given = c("Michael", "P."),
                      family = "Fay",
                      role = c("aut", "cre"),
                      email = "mfay@niaid.nih.gov"))
as necessary.
Maintainer: ‘Dave Hunter <dhunter@westmont.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("David", "J."),
                      family = "Hunter",
                      role = "aut"),
               person(given = "McKalie",
                      family = "Drown",
                      role = "aut"),
               person(given = "Dave",
                      family = "Hunter",
                      role = "cre",
                      email = "dhunter@westmont.edu"))
as necessary.
Maintainer: ‘Yingjie Feng <fengyingjiepku@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Matias", "D."),
                      family = "Cattaneo",
                      role = "aut"),
               person(given = c("Richard", "K."),
                      family = "Crump",
                      role = "aut"),
               person(given = c("Max", "H."),
                      family = "Farrell",
                      role = "aut"),
               person(given = "Yingjie",
                      family = "Feng",
                      role = c("aut", "cre"),
                      email = "fengyingjiepku@gmail.com"))
as necessary.
Maintainer: ‘Chapman Siu <chpmn.siu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chapman",
                    family = "Siu",
                    role = c("aut", "cre"),
                    email = "chpmn.siu@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bbassets.R’
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Roberto Serrano-Notivoli <roberto.serrano@unizar.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Roberto",
                    family = "Serrano-Notivoli",
                    role = c("aut", "cre"),
                    email = "roberto.serrano@unizar.es")
as necessary.
Package required but not available: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marcelo Ponce <m.ponce@utoronto.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marcelo",
                    family = "Ponce",
                    role = c("aut", "cre"),
                    email = "m.ponce@utoronto.ca")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'devtools', 'roxygen2', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'BiocStyle', 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'yaml', 'rmarkdown'

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Found the following significant warnings:
  ../src/inc/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  ../src/inc/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  ../src/inc/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BioCro.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-15 (Debian 15.2.0-9) 15.2.0’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Federico Calboli <f.calboli@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alessio",
                      family = "Boattini",
                      role = "aut"),
               person(given = c("Federico", "C.", "F.", "Calboli;", "Vincente", "Canto", "Cassola", "together", "with", "Martin", "Maechler", "authored", "the", "function"),
                      family = "mtx.exp.",
                      role = "aut"),
               person(given = "Federico",
                      family = "Calboli",
                      role = "cre",
                      email = "f.calboli@gmail.com"))
as necessary.
Package required but not available: ‘Rcmdr’

Packages suggested but not available for checking:
  'vegan3d', 'rgl', 'gam', 'ENMeval', 'envirem'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'golem', 'bsplus', 'mixtools', 'rhandsontable', 'config', 'rmarkdown'

Packages suggested but not available for checking:
  'covr', 'knitr', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/biogas_quick_start.Rnw’
   ‘inst/doc/calcBgMan_function.Rnw’
   ‘inst/doc/calcBgVol_function.Rnw’
   ‘inst/doc/predBg_function.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Michal Burdukiewicz <michalburdukiewicz@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) calc_ed.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_pi.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_si.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) cluster_reg_exp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘EBImage’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Lester L. Yuan <yuan.lester@epa.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Lester", "L."),
                    family = "Yuan",
                    role = c("aut", "cre"),
                    email = "yuan.lester@epa.gov")
as necessary.
Package required but not available: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zachary Colburn <zcolburn@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Zachary",
                    family = "Colburn",
                    role = c("aut", "cre"),
                    email = "zcolburn@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'WGCNA', 'htmlwidgets', 'wordcloud2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc', 'pkgdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running examples in ‘biometrics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: domvar
> ### Title: Function to compute a dominant stand-level variable based on a
> ###   sample plot data.
> ### Aliases: domvar
> 
> ### ** Examples
> 
> 
> ##Creates a fake dataframe
> set.seed(45)
> x <- round(rnorm(20,mean=45,sd=10),1); y=round(1.3+35*(1-exp(-.07*x)),1)
> df<-data.frame(dap=x,atot=y)
> head(df)
   dap atot
1 48.4 35.1
2 38.0 33.9
3 41.2 34.3
4 37.5 33.8
5 36.0 33.5
6 41.7 34.4
> datana::descstat(df)
Error in loadNamespace(x) : there is no package called ‘datana’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

Package which this enhances but not available for checking: ‘asreml’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'Hmisc', 'gam', 'ENMeval', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Found the following files/directories:
  ‘GuloGulo’
Cannot process vignettes
Packages suggested but not available for checking:
  'DataExplorer', 'DT', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘BioMonTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: markExcluded
> ### Title: Mark "exclude" (non-distinct / non-unique / ambiguous) taxa
> ### Aliases: markExcluded
> 
> ### ** Examples
> 
> 
> # Packages
> library(readxl)
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(lazyeval)
> library(knitr)
Error in library(knitr) : there is no package called ‘knitr’
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Giorgio Valentini<valentini@di.unimi.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Giorgio",
                      family = "Valentini",
                      role = c("aut", "cre"),
                      email = "valentini@di.unimi.it"),
               person(given = c("Matteo", "Re", "--", "Universita'", "degli", "Studi", "di"),
                      family = "Milano",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'GPareto'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘survminer’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Paula Saavedra-Nieves <paula.saavedra@usc.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alejandro",
                      family = "Saavedra-Nieves",
                      role = "aut"),
               person(given = "Paula",
                      family = "Saavedra-Nieves",
                      role = c("aut", "cre"),
                      email = "paula.saavedra@usc.es"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rmarkdown’

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Piyal Karunarathne <piyalkarumail@yahoo.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Marie Chabbert <marie.chabbert@univ-angers.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Julien", "Pele", "with", "Jean-Michel"),
                      family = "Becu",
                      role = "aut"),
               person(given = c("Rym", "Ben"),
                      family = "Boubaker",
                      role = "aut"),
               person(given = "Herve",
                      family = "Abdi",
                      role = "aut"),
               person(given = "Marie",
                      family = "Chabbert",
                      role = c("aut", "cre"),
                      email = "marie.chabbert@univ-angers.fr"))
as necessary.
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘fda.usc’

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Antonio Guerrero <jaguerrero@correo.uaa.mx>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "J.A.",
                      family = "Guerrero",
                      role = "aut"),
               person(given = "J.E.",
                      family = "Macias-Diaz",
                      role = "aut"),
               person(given = "Antonio",
                      family = "Guerrero",
                      role = "cre",
                      email = "jaguerrero@correo.uaa.mx"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Stefan Michiels <stefan.michiels@gustaveroussy.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Nils",
                      family = "Ternes",
                      role = "aut"),
               person(given = "Federico",
                      family = "Rotolo",
                      role = "aut"),
               person(given = "Stefan",
                      family = "Michiels",
                      role = c("aut", "cre"),
                      email = "stefan.michiels@gustaveroussy.fr"))
as necessary.
Packages required but not available: 'devtools', 'plsRcox', 'survAUC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Rob Knell <r.knell@qmul.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Rob",
                    family = "Knell",
                    role = c("aut", "cre"),
                    email = "r.knell@qmul.ac.uk")
as necessary.
Package required but not available: ‘learnr’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Package suggested but not available for checking: ‘covr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dr Rob Briers <r.briers@napier.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Dr", "Rob"),
                    family = "Briers",
                    role = c("aut", "cre"),
                    email = "r.briers@napier.ac.uk")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'quarto', 'knitr'

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'soilphysics', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tim Hulsen <thulsen@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘r2d3’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Michael Seo <swj8874@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'htmlwidgets', 'knitr', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ana Belen Nieto Librero <ananieto@usal.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ana", "Belen", "Nieto"),
                      family = "Librero",
                      role = c("aut", "cre"),
                      email = "ananieto@usal.es"),
               person(given = "Adelaide",
                      family = "Freitas",
                      role = "aut",
                      email = "Adelaide@ua.pt"))
as necessary.
Packages required but not available: 'matlib', 'rgl', 'shapes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rgl', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘AoD.Rd’ ‘AoD.biplot.Rd’ ‘CA.Rd’ ‘CA.biplot.Rd’ ‘CLPs.Rd’ ‘CVA.Rd’
    ‘CVA.biplot.Rd’ ‘PCA.Rd’ ‘PCA.biplot.Rd’ ‘PCO.Rd’ ‘PCO.biplot.Rd’
    ‘alpha.bags.Rd’ ‘axes.Rd’ ‘axes_coordinates.Rd’ ‘biplot.R’
    ‘biplot.Rd’ ‘classification.Rd’ ‘classify.Rd’ ‘density1D.Rd’
    ‘density2D.Rd’ ‘ellipses.Rd’ ‘fit.measures.Rd’ ‘interpolate.Rd’
    ‘legend.type.Rd’ ‘means.Rd’ ‘newaxes.Rd’ ‘newsamples.Rd’
    ‘plot.biplot.Rd’ ‘prediction.Rd’ ‘print.biplot.Rd’ ‘reflect.Rd’
    ‘regress.Rd’ ‘regress.biplot.Rd’ ‘rotate.Rd’ ‘samples.Rd’
    ‘summary.biplot.Rd’ ‘translate_axes.R’ ‘translate_axes.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'roxygen2', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Fraenzi Korner-Nievergelt <fraenzi.korner@vogelwarte.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Fraenzi",
                      family = "Korner-Nievergelt",
                      role = c("aut", "cre"),
                      email = "fraenzi.korner@vogelwarte.ch"),
               person(given = "Rob",
                      family = "Robinson",
                      role = "aut"))
as necessary.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Matthew A. Birk <matthewabirk@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Matthew", "A."),
                    family = "Birk",
                    role = c("aut", "cre"),
                    email = "matthewabirk@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mark Wappett <m.wappett@qub.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mark",
                    family = "Wappett",
                    role = c("aut", "cre"),
                    email = "m.wappett@qub.ac.uk")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Carine Legrand <c.legrand@dkfz.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "C",
                      family = "Legrand",
                      role = "aut"),
               person(given = "Carine",
                      family = "Legrand",
                      role = "cre",
                      email = "c.legrand@dkfz.de"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘yaml’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'tidyquant'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bits_to_raw.Rd’ ‘bitstream-ints.R’ ‘bitstream-uints-exp-golomb.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rrtable', 'table1'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jia-Han Shih <tommy355097@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jia-Han",
                      family = "Shih",
                      role = c("aut", "cre"),
                      email = "tommy355097@gmail.com"),
               person(given = "Wei",
                      family = "Lee",
                      role = "aut"))
as necessary.
Maintainer: ‘Alessandro Barbiero <alessandro.barbiero@unimi.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alessandro",
                    family = "Barbiero",
                    role = c("aut", "cre"),
                    email = "alessandro.barbiero@unimi.it")
as necessary.
Maintainer: ‘Ran Gao <rgao8@uic.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hakan",
                      family = "Demirtas",
                      role = "aut"),
               person(given = "Rawan",
                      family = "Allozi",
                      role = "aut"),
               person(given = "Ran",
                      family = "Gao",
                      role = c("aut", "cre"),
                      email = "rgao8@uic.edu"))
as necessary.
Maintainer: ‘Jo Hardin <jo.hardin@pomona.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jo",
                    family = "Hardin",
                    role = c("aut", "cre"),
                    email = "jo.hardin@pomona.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘DHARMa’

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jan Klaschka <klaschka@cs.cas.cz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jan",
                    family = "Klaschka",
                    role = c("aut", "cre"),
                    email = "klaschka@cs.cas.cz")
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘binom.blaker.VHadj.limits.Rd’:
    http://dx.doi.org/10.1080/03610918.2014.911900
  File ‘binom.blaker.limits.Rd’:
    http://dx.doi.org/10.1080/03610918.2014.911900
  File ‘poisson.blaker.limits.Rd’:
    http://dx.doi.org/10.1080/03610918.2014.911900
Maintainer: ‘Bernhard Lehnert <bernhard.lehnert@uni-greifswald.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bernhard",
                    family = "Lehnert",
                    role = c("aut", "cre"),
                    email = "bernhard.lehnert@uni-greifswald.de")
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘BlandAltmanLeh-package.Rd’:
    \keyword{ measurement precision, test-retest relia [TRUNCATED]
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'ggExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rmarkdown’

Packages suggested but not available for checking:
  'covr', 'keyring', 'knitr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fBasics', 'fMultivar', 'fPortfolio', 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'INLA', 'knitr', 'rmarkdown', 'survHEhmc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) RLdata500.Rd:8: Lost braces
     8 | A data frame with five variables: \code{fname_c1},\code{lname_c1},  \code{by}, code{bm}, \code{bd}.
       |                                                                                    ^
checkRd: (-1) identity.RLdata500.Rd:15: Lost braces
    15 | format A vector that contains the code{id}
       |                                       ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

Package in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Fraenzi Korner-Nievergelt <fraenzi.korner@oikostat.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Fraenzi",
                      family = "Korner-Nievergelt",
                      role = c("aut", "cre"),
                      email = "fraenzi.korner@oikostat.ch"),
               person(given = "Tobias",
                      family = "Roth",
                      role = "aut"),
               person(given = "Stefanie",
                      family = "von Felten",
                      role = "aut"),
               person(given = "Jerome",
                      family = "Guelat",
                      role = "aut"),
               person(given = "Bettina",
                      family = "Almasi",
                      role = "aut"),
               person(given = "Pius",
                      family = "Korner-Nievergelt",
                      role = "aut"))
as necessary.
Maintainer: ‘S.Kovalchik <s.a.kovalchik@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "S.",
                      family = "Kovalchik",
                      role = "aut"),
               person(family = "S.Kovalchik",
                      role = "cre",
                      email = "s.a.kovalchik@gmail.com"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Marie Perrot-Dockès <marie.perrocks@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "M.",
                      family = "Perrot-Dock\\`es",
                      role = "aut"),
               person(given = "C.",
                      family = "Lévy-Leduc",
                      role = "aut"),
               person(given = "Marie",
                      family = "Perrot-Dockès",
                      role = "cre",
                      email = "marie.perrocks@gmail.com"))
as necessary.

The Description field contains
  in the paper Perrot-Dockès et al. (2019) <arXiv:1806.10093>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'tmap', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Marvin N. Wright <cran@wrig.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Roman",
                      family = "Hornung",
                      role = "aut"),
               person(given = c("Marvin", "N."),
                      family = "Wright",
                      role = c("aut", "cre"),
                      email = "cran@wrig.de"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Emanuele Cordano <emanuele.cordano@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Emanuele",
                    family = "Cordano",
                    role = c("aut", "cre"),
                    email = "emanuele.cordano@gmail.com")
as necessary.

The Description field contains
  (http://en.wikipedia.org/wiki/Block_matrix). The block matrix is here
Please enclose URLs in angle brackets (<...>).
Maintainer: ‘Fabio Ashtar Telarico <telaricof@fdv.uni-lj.si>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available:
  'DT', 'htmlwidgets', 'shinybusy', 'visNetwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jean-Benoist Leger <jbleger@hds.utc.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jean-Benoist",
                      family = "Leger",
                      role = c("aut", "cre"),
                      email = "jbleger@hds.utc.fr"),
               person(given = "Pierre",
                      family = "Barbillon",
                      role = "aut",
                      email = "pierre.barbillon@agroparistech.fr"),
               person(given = "Julien",
                      family = "Chiquet",
                      role = "aut",
                      email = "julien.chiquet@inrae.fr"))
as necessary.
Maintainer: ‘Greg Snow <538280@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Greg",
                    family = "Snow",
                    role = c("aut", "cre"),
                    email = "538280@gmail.com")
as necessary.
Package required but not available: ‘DT’

Packages suggested but not available for checking:
  'shinytest2', 'roxy.shinylive', 'knitr', 'rmarkdown', 'quarto'

VignetteBuilder package required for checking but not installed: ‘quarto’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Rodney Edmondson <rodney.edmondson@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("R.", "N."),
                      family = "Edmondson.",
                      role = "aut"),
               person(given = "Rodney",
                      family = "Edmondson",
                      role = "cre",
                      email = "rodney.edmondson@gmail.com"))
as necessary.
checkRd: (-1) durban.Rd:16: Lost braces; missing escapes or markup?
    16 | This data set was obtained from the durban.rowcol {agridat} example in package 'agridat' 
       |                                                   ^
checkRd: (-1) fraction.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘assg2xBalance.R’
checkRd: (-1) estimate_density.Rd:25: Lost braces; missing escapes or markup?
    25 | evenly spaced points between \code{min} and {max}.
       |                                             ^
Packages required but not available:
  'bookdown', 'knitr', 'rmarkdown', 'yaml'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Daniel Brunner <daniel.brunner@hhu.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Daniel",
                      family = "Brunner",
                      role = c("aut", "cre"),
                      email = "daniel.brunner@hhu.de",
                      comment = "aut"),
               person(given = "Constantin",
                      family = "Weiser",
                      role = "aut",
                      comment = "ctr"),
               person(given = "Andre",
                      family = "Romahn",
                      role = "aut",
                      comment = "ctr"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Furong Sun <furongs@vt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Furong",
                      family = "Sun",
                      role = c("aut", "cre"),
                      email = "furongs@vt.edu"),
               person(given = "Zhonggai",
                      family = "Li",
                      role = "aut",
                      email = "zli@bostonbiomedical.com"))
as necessary.
Maintainer: ‘Christoph Ritschel <christoph.ritschel@met.fu-berlin.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christoph",
                    family = "Ritschel",
                    role = c("aut", "cre"),
                    email = "christoph.ritschel@met.fu-berlin.de")
as necessary.
Maintainer: ‘Paulino Perez Rodriguez <perpdgo@colpos.mx>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Gustavo", "de", "los"),
                      family = "Campos",
                      role = "aut"),
               person(given = c("Paulino", "Perez"),
                      family = "Rodriguez,",
                      role = "aut"),
               person(given = c("Paulino", "Perez"),
                      family = "Rodriguez",
                      role = "cre",
                      email = "perpdgo@colpos.mx"))
as necessary.
Maintainer: ‘Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kartikeya",
                    family = "Bolar",
                    role = c("aut", "cre"),
                    email = "kartikeya.bolar@tapmi.edu.in")
as necessary.
Packages required but not available: 'rmarkdown', 'rhandsontable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kartikeya",
                    family = "Bolar",
                    role = c("aut", "cre"),
                    email = "kartikeya.bolar@tapmi.edu.in")
as necessary.
Packages required but not available: 'rmarkdown', 'rhandsontable'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
'::' or ':::' imports not declared from:
  ‘abind’ ‘abjutils’ ‘bayesplot’ ‘devtools’ ‘dplyr’ ‘fs’ ‘furrr’
  ‘knitr’ ‘purrr’ ‘readr’ ‘stringr’ ‘tibble’ ‘tidyr’
'library' or 'require' calls not declared from:
  ‘future’ ‘tidyverse’
Package required but not available: ‘leaflet’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Specified C++11: support will be removed soon
Maintainer: ‘Michael Turchin <mturchin20@uchicago.edu>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘GetModelPriorMatrix.Rd’:
    https://doi.org/10.1371/journal.pone.0065245
  File ‘GlobalLipids2013.GWASsnps.Rd’:
    https://doi.org/10.1038/ng.2797
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) dot-pred_array_to_df.Rd:20: Lost braces; missing escapes or markup?
    20 | Helper function for as.data.frame.{fitted, forecast}. Converts predictive array to data.frame.
       |                                   ^
Package required but not available: ‘GGUM’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Reza Mohammadi <a.mohammadi@uva.nl>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Running examples in ‘bmlm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mlm_path_plot
> ### Title: Plot 'bmlm"s mediation model as a path diagram
> ### Aliases: mlm_path_plot
> 
> ### ** Examples
> 
> # Draw a template path diagram of the mediation model
> mlm_path_plot()
Error: qgraph package needed for this function. Please install it.
Execution halted
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
No news entries found.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michele Scandola <michele.scandola@univr.it>’

The BugReports field in DESCRIPTION has
  https://github.com/michelescandola/bmscstan
which should likely be
  https://github.com/michelescandola/bmscstan/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) BMSC_pareto_k_table.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:60-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:64-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:67-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Stefan Zeugner <stefan.zeugner@ec.europa.eu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Martin",
                      family = "Feldkircher",
                      role = "aut"),
               person(given = "Stefan",
                      family = "Zeugner",
                      role = c("aut", "cre"),
                      email = "stefan.zeugner@ec.europa.eu"),
               person(given = "Paul",
                      family = "Hofmarcher",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'CARBayes', 'CARBayesST'

Packages suggested but not available for checking:
  'INLA', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘qgraph’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

Packages in Depends/Imports which should probably only be in LinkingTo:
  ‘BH’ ‘RcppEigen’
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘bnns.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Marvin N. Wright <marv@wrig.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Marvin", "N."),
                    family = "Wright",
                    role = c("aut", "cre"),
                    email = "marv@wrig.de")
as necessary.
Package required but not available: ‘pec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Elias Carvalho <ecacarva@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Elias",
                      family = "Carvalho",
                      role = c("aut", "cre"),
                      email = "ecacarva@gmail.com"),
               person(given = c("Joao", "R", "N"),
                      family = "Vissoci",
                      role = "aut"),
               person(given = "Luciano",
                      family = "Andrade",
                      role = "aut"),
               person(given = "Wagner",
                      family = "Machado",
                      role = "aut"),
               person(given = c("Emerson", "P"),
                      family = "Cabrera",
                      role = "aut"),
               person(given = c("Julio", "C"),
                      family = "Nievola",
                      role = "aut"))
as necessary.
Packages required but not available: 'semPlot', 'xlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Alejandro Ochoa <alejandro.ochoa@duke.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘David Alejandro Martell Juarez <alex91599@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(family = "Martell-Juarez",
                      role = "aut"),
               person(given = c("D.A.", "&"),
                      family = "Nieto-Barajas",
                      role = "aut"),
               person(family = "L.E.",
                      role = "aut"),
               person(given = c("David", "Alejandro", "Martell"),
                      family = "Juarez",
                      role = "cre",
                      email = "alex91599@gmail.com"))
as necessary.
Packages required but not available: 'DT', 'qgraph'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Joe Suzuki <j-suzuki@sigmath.es.osaka-u.ac.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Joe",
                      family = "Suzuki",
                      role = c("aut", "cre"),
                      email = "j-suzuki@sigmath.es.osaka-u.ac.jp"),
               person(given = "Jun",
                      family = "Kawahara",
                      role = "aut"))
as necessary.
Maintainer: ‘Georgios Papageorgiou <gpapageo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Georgios",
                    family = "Papageorgiou",
                    role = c("aut", "cre"),
                    email = "gpapageo@gmail.com")
as necessary.
Package required but not available: ‘threejs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'qgraph', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package required but not available: ‘visNetwork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Brian J. Smith <brian-j-smith@uiowa.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |               ^
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |                                             ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) refAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) refAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:13-14: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gleidson Mendes Rebouças <gleidsonreboucas@uern.br>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Gleidson", "Mendes"),
                      family = "Rebouças",
                      role = c("aut", "cre"),
                      email = "gleidsonreboucas@uern.br"),
               person(given = c("Thiago", "Renee"),
                      family = "Felipe",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'usethis', 'adiposerefdata', 'musclerefdata', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mario Annau <mario.annau@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("See", "AUTHORS"),
                      family = "file.",
                      role = "aut"),
               person(given = "Mario",
                      family = "Annau",
                      role = "cre",
                      email = "mario.annau@gmail.com"))
as necessary.
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'gt', 'DT', 'plotly', 'rhandsontable'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ying Yuan <yyuan@mdanderson.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ying",
                      family = "Yuan",
                      role = c("aut", "cre"),
                      email = "yyuan@mdanderson.org"),
               person(given = "Suyu",
                      family = "Liu",
                      role = "aut"))
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘skimr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘James Curran <j.curran@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "James",
                    family = "Curran",
                    role = c("aut", "cre"),
                    email = "j.curran@auckland.ac.nz")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rgl', 'nat'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dongmei Li <dongmei_li@urmc.rochester.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dongmei",
                    family = "Li",
                    role = c("aut", "cre"),
                    email = "dongmei_li@urmc.rochester.edu")
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘BonEV-package.Rd’:
    \keyword{multiple testing procedure, false discove [TRUNCATED]
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'fGarch', 'fBasics'

Depends: includes the non-default packages:
  'tseries', 'fGarch', 'timeSeries', 'timeDate', 'fBasics', 'geoR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

Packages suggested but not available for checking:
  'downlit', 'htmlwidgets', 'rsconnect', 'tufte'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'factoextra', 'FactoMineR', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Levi McClenny <levimcclenny@tamu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Levi",
                      family = "McClenny",
                      role = c("aut", "cre"),
                      email = "levimcclenny@tamu.edu"),
               person(given = "Mahdi",
                      family = "Imani",
                      role = "aut"),
               person(given = "Ulisses",
                      family = "Braga-Neto",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'flow', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Amol Pande <amoljpande@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Amol",
                      family = "Pande",
                      role = c("aut", "cre"),
                      email = "amoljpande@gmail.com"),
               person(given = "Hemant",
                      family = "Ishwaran",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Found the following significant warnings:
  Warning: replacing previous import ‘mclust::count’ by ‘plyr::count’ when loading ‘bootcluster’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bootcluster.Rcheck/00install.out’ for details.
Maintainer: ‘Marc Henrion <mhenrion@mlw.mw>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Gianmarco Vacca <gianmarco.vacca@unicatt.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gianmarco",
                      family = "Vacca",
                      role = c("aut", "cre"),
                      email = "gianmarco.vacca@unicatt.it"),
               person(given = "Stefano",
                      family = "Bertelli",
                      role = "aut"))
as necessary.
Package required but not available: ‘usethis’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zhengguo Xu <zhengguoxu@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'roxygen2', 'pkgdown', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'rmarkdown'

Package suggested but not available for checking: ‘roxygen2’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ari B. Friedman <abfriedman@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Keith", "A."),
                      family = "Marill",
                      role = "aut"),
               person(given = c("Ari", "B."),
                      family = "Friedman",
                      role = c("aut", "cre"),
                      email = "abfriedman@gmail.com"))
as necessary.
Maintainer: ‘Samarendra Das <samarendra4849@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Samarendra",
                    family = "Das",
                    role = c("aut", "cre"),
                    email = "samarendra4849@gmail.com")
as necessary.
Packages required but not available:
  'IsingFit', 'qgraph', 'mgm', 'NetworkToolbox', 'networktools'

Packages suggested but not available for checking: 'GGMncv', 'graphicalVAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'prettydoc', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jae H. Kim <jaekim8080@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jae.", "H."),
                      family = "Kim",
                      role = "aut",
                      email = "jaekim8080@gmail.com"),
               person(given = c("Jae", "H."),
                      family = "Kim",
                      role = "cre",
                      email = "jaekim8080@gmail.com"))
as necessary.
Packages required but not available: 'rms', 'gt', 'flextable'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Benjamin Baumgartner <benjamin@baumgrt.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Benjamin",
                      family = "Baumgartner",
                      role = c("aut", "cre"),
                      email = "benjamin@baumgrt.com"),
               person(given = "Riccardo",
                      family = "Gatto",
                      role = "aut",
                      email = "gatto@stat.unibe.ch"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dimitris",
                    family = "Rizopoulos",
                    role = c("aut", "cre"),
                    email = "d.rizopoulos@erasmusmc.nl")
as necessary.
'library' or 'require' call not declared from: ‘survival’
Maintainer: ‘Scott Ritchie <sritchie73@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Qin", "Qin"),
                      family = "Huang",
                      role = "aut"),
               person(given = "Scott",
                      family = "Ritchie",
                      role = c("aut", "cre"),
                      email = "sritchie73@gmail.com"))
as necessary.
Maintainer: ‘Scott Kostyshak <scott.kostyshak@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "S",
                      family = "original",
                      role = "aut"),
               person(given = "from",
                      family = "StatLib",
                      role = "aut"),
               person(given = c("by", "Rob", "Tibshirani.", "R", "port", "by", "Friedrich"),
                      family = "Leisch.",
                      role = "aut"),
               person(given = "Scott",
                      family = "Kostyshak",
                      role = "cre",
                      email = "scott.kostyshak@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘npboottprm’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Guy Nason <g.nason@imperial.ac.uk>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Jeffrey A. Boatman <jeffrey.boatman@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jeffrey", "A."),
                      family = "Boatman",
                      role = c("aut", "cre"),
                      email = "jeffrey.boatman@gmail.com"),
               person(given = c("David", "M."),
                      family = "Vock",
                      role = "aut"),
               person(given = c("Joseph", "S."),
                      family = "Koopmeiners",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Raphaël Clifford <clifford@cs.bris.ac.uk>’

The Description field contains
  (2017) <arXiv:1706.01260>. Also provides functions for generating
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Pierre Lefeuvre <pierre.lefeuvre@cirad.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Pierre",
                    family = "Lefeuvre",
                    role = c("aut", "cre"),
                    email = "pierre.lefeuvre@cirad.fr")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'prettydoc', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Sen Tian <stian@stern.nyu.edu>’

The Description field contains
  for Subset Selection in Least Squares Regression", <arXiv:1911.10191>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Emanuele Cordano <emanuele.cordano@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Emanuele",
                    family = "Cordano",
                    role = c("aut", "cre"),
                    email = "emanuele.cordano@gmail.com")
as necessary.
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/PlottingGuide.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘lintr’

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'rhino', 'spelling'

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Shinichiro Tomizono <cowares@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Shinichiro",
                    family = "Tomizono",
                    role = c("aut", "cre"),
                    email = "cowares@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'usethis', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Michael P. Fay <mfay@niaid.nih.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Michael", "P."),
                      family = "Fay",
                      role = c("aut", "cre"),
                      email = "mfay@niaid.nih.gov"),
               person(given = "Allyson",
                      family = "Mateja",
                      role = "ctb"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Davide Buttarazzi <davidebuttarazzi@outlook.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Davide",
                    family = "Buttarazzi",
                    role = c("aut", "cre"),
                    email = "davidebuttarazzi@outlook.com")
as necessary.
Packages required but not available:
  'DiagrammeR', 'htmlwidgets', 'DT', 'knitr'

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jianzhao Gao and Xiaodan Fan <gaojz@nankai.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jianzhao",
                      family = "Gao",
                      role = c("aut", "cre"),
                      email = "gaojz@nankai.edu.cn"),
               person(given = "Linghao",
                      family = "Shen",
                      role = "aut"),
               person(given = "Xiaodan",
                      family = "Fan",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘sim_dat_one_trial_exp_covar.R’ ‘sim_dat_one_trial_exp_nocovar.R’
Maintainer: ‘Laura D'Angelo <laura.dangelo@live.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Laura",
                    family = "D'Angelo",
                    role = c("aut", "cre"),
                    email = "laura.dangelo@live.com")
as necessary.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bqtl.Rcheck/00install.out’ for details.
Package required but not available: ‘survminer’

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘fbst’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DT'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'bookdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/BradleyTerry.Rmd’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ville Satopää <ville.satopaa@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rgl', 'brainR', 'knitr'

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘BranchGLM.R’ ‘BranchGLMTable.R’ ‘VariableImportance.R’
    ‘VariableImportance.boot.R’ ‘summaryBranchGLMVS.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Camilo Jose Torres-Jimenez <cjtorresj@unal.edu.co>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Camilo", "Jose"),
                    family = "Torres-Jimenez",
                    role = c("aut", "cre"),
                    email = "cjtorresj@unal.edu.co")
as necessary.
Package required but not available: ‘yaml’

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

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

Packages suggested but not available for checking:
  'flextable', 'ggiraph', 'gt', 'knitr', 'plotly', 'rmarkdown',
  'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Benjamin Schlegel <kontakt@benjaminschlegel.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Benjamin",
                      family = "Schlegel",
                      role = c("aut", "cre"),
                      email = "kontakt@benjaminschlegel.ch"),
               person(given = "Marco",
                      family = "Steenbergen",
                      role = "aut"))
as necessary.
Maintainer: ‘Mike Lee <random.deviate@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mike",
                    family = "Lee",
                    role = c("aut", "cre"),
                    email = "random.deviate@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'tidyverse', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
No news entries found.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Amy D Willis <adwillis@uw.edu>’

The Description field contains
  <doi:10.1111/rssc.12206>, and Willis (2016) <arXiv:1604.02598>, as well
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Santiago I. Hurtado <santih@carina.fcaglp.unlp.edu.ar>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Santiago", "I."),
                    family = "Hurtado",
                    role = c("cre", "aut"),
                    email = "santih@carina.fcaglp.unlp.edu.ar")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Christian Graul <christian.graul@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Christian",
                      family = "Graul",
                      role = c("aut", "cre"),
                      email = "christian.graul@gmail.com"),
               person(given = "Carsten",
                      family = "Poppinga",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'gtsummary', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Andrew McKenzie <amckenz@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Andrew",
                      family = "McKenzie",
                      role = c("aut", "cre"),
                      email = "amckenz@gmail.com"),
               person(given = "Minghui",
                      family = "Wang",
                      role = "aut"),
               person(given = "Bin",
                      family = "Zhang",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'bookdown', 'DT', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rstanarm', 'cmdstanr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Aurora Torrente <etorrent@est-econ.uc3m.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Javier", "Albert"),
                      family = "Smet",
                      role = "aut",
                      email = "javas@kth.se"),
               person(given = c("Aurora", "Torrente.", "Alice"),
                      family = "Parodi",
                      role = "aut",
                      email = "etorrent@est-econ.uc3m.es"),
               person(given = "Mirco",
                      family = "Patriarca",
                      role = "aut"),
               person(given = "Laura",
                      family = "Sangalli",
                      role = "aut"),
               person(given = "Piercesare",
                      family = "Secchi",
                      role = "aut"),
               person(given = "Simone",
                      family = "Vantini",
                      role = "aut"),
               person(given = "Valeria",
                      family = "Vitelli",
                      role = "aut"),
               person(given = "as",
                      family = "contributors.",
                      role = "aut"),
               person(given = "Aurora",
                      family = "Torrente",
                      role = "cre",
                      email = "etorrent@est-econ.uc3m.es"))
as necessary.
Package required but not available: ‘Hmisc’

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

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mauricio Sadinle <msadinle@uw.edu>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘BRL.Rd’:
    https://doi.org/10.1080/01621459.2016.1148612
  File ‘bipartiteGibbs.Rd’:
    https://doi.org/10.1080/01621459.2016.1148612
  File ‘compareRecords.Rd’:
    https://doi.org/10.1080/01621459.2016.1148612
  File ‘linkRecords.Rd’:
    https://doi.org/10.1080/01621459.2016.1148612
  File ‘twoFiles.Rd’:
    https://doi.org/10.1080/01621459.2016.1148612
Maintainer: ‘Mark Clements <mark.clements@ki.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Linbo",
                      family = "Wang",
                      role = "aut"),
               person(given = "Mark",
                      family = "Clements",
                      role = c("aut", "cre"),
                      email = "mark.clements@ki.se"),
               person(given = "Thomas",
                      family = "Richardson",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'gt', 'gtsummary', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘brm_archetype_average_cells.Rd’ ‘brm_archetype_average_effects.Rd’
    ‘brm_archetype_cells.Rd’ ‘brm_archetype_effects.Rd’
    ‘brm_archetype_successive_cells.Rd’
    ‘brm_archetype_successive_effects.Rd’ ‘brm_formula.Rd’
    ‘brm_prior_archetype.Rd’ ‘brm_prior_label.Rd’ ‘brm_prior_template.Rd’
    ‘brm_recenter_nuisance.Rd’ ‘summary.brms_mmrm_archetype.Rd’
    ‘utils_archetype.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'cmdstanr', 'projpred', 'shinystan', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Robin K. S. Hankin <hankin.robin@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'bookdown', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/broman.Rcheck/00install.out’ for details.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'gam', 'gt', 'gtsummary', 'knitr', 'rmarkdown', 'rstanarm',
  'spelling', 'tidycmprsk'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘broom.helpers-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: model_get_n
> ### Title: Get the number of observations
> ### Aliases: model_get_n model_get_n.default model_get_n.glm
> ###   model_get_n.glmerMod model_get_n.multinom model_get_n.LORgee
> ###   model_get_n.coxph model_get_n.survreg model_get_n.model_fit
> ###   model_get_n.tidycrr
> 
> ### ** Examples
> 
> lm(hp ~ mpg + factor(cyl) + disp:hp, mtcars) |>
+   model_get_n()
# A tibble: 6 × 2
  term         n_obs
  <chr>        <dbl>
1 (Intercept)     32
2 mpg             32
3 factor(cyl)6     7
4 factor(cyl)8    14
5 hp:disp         32
6 factor(cyl)4    11
> 
> mod <- glm(
+   response ~ stage * grade + trt,
+   gtsummary::trial,
+   family = binomial,
+   contrasts = list(stage = contr.sum, grade = contr.treatment(3, 2), trt = "contr.SAS")
+ )
Error in loadNamespace(x) : there is no package called ‘gtsummary’
Calls: glm ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'glmmADMB', 'mediation', 'rstanarm', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Author field differs from that derived from Authors@R
  Author:    ‘Ben Bolker [aut, cre] (<https://orcid.org/0000-0002-2127-0443>), David Robinson [aut], Dieter Menne [ctb], Jonah Gabry [ctb], Paul Buerkner [ctb], Christopher Hua [ctb], William Petry [ctb] (<https://orcid.org/0000-0002-5230-5987>), Joshua Wiley [ctb] (<https://orcid.org/0000-0002-0271-6702>), Patrick Kennedy [ctb], Eduard Szöcs [ctb] (<https://orcid.org/0000-0001-5376-1194>, BASF SE), Indrajeet Patil [ctb], Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>), Bill Denney [ctb], Cory Brunson [ctb], Joe Wasserman [ctb] (<https://orcid.org/0000-0002-9705-1853>), Alexey Stukalov [ctb], Matthieu Bruneaux [ctb]’
  Authors@R: ‘Ben Bolker [aut, cre] (ORCID: <https://orcid.org/0000-0002-2127-0443>), David Robinson [aut], Dieter Menne [ctb], Jonah Gabry [ctb], Paul Buerkner [ctb], Christopher Hua [ctb], William Petry [ctb] (ORCID: <https://orcid.org/0000-0002-5230-5987>), Joshua Wiley [ctb] (ORCID: <https://orcid.org/0000-0002-0271-6702>), Patrick Kennedy [ctb], Eduard Szöcs [ctb] (ORCID: <https://orcid.org/0000-0001-5376-1194>, sponsor: BASF SE), Indrajeet Patil [ctb], Vincent Arel-Bundock [ctb] (ORCID: <https://orcid.org/0000-0003-2042-7063>), Bill Denney [ctb], Cory Brunson [ctb], Joe Wasserman [ctb] (ORCID: <https://orcid.org/0000-0002-9705-1853>), Alexey Stukalov [ctb], Matthieu Bruneaux [ctb]’

  Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘glmm_tidiers.R’ ‘rstanarm_tidiers.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'btergm', 'covr', 'epiR', 'ergm', 'gam', 'Hmisc', 'knitr',
  'mediation', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Maintainer: ‘Yan Zhao <yanzhao3@illinois.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Smruti",
                      family = "Padhy",
                      role = "aut"),
               person(given = "Rob",
                      family = "Kooper",
                      role = "aut"),
               person(given = "Yan",
                      family = "Zhao",
                      role = c("aut", "cre"),
                      email = "yanzhao3@illinois.edu"))
as necessary.
Maintainer: ‘Rahim Alhamzawi  (University of Al-Qadisiyah) <rahim.alhamzawi@qu.edu.iq>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Rahim",
                    family = "Alhamzawi",
                    role = c("aut", "cre"),
                    email = "rahim.alhamzawi@qu.edu.iq")
as necessary.
Package required but not available: ‘RcmdrMisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘census2021.Rd’
Running examples in ‘bruneimap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: census2021
> ### Title: Brunei census data 2021
> ### Aliases: census2021
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Joshua Ray Tanzer <jtanzer@lifespan.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Joshua", "Ray"),
                    family = "Tanzer",
                    role = c("aut", "cre"),
                    email = "jtanzer@lifespan.org")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'DT', 'golem', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Frank Schaarschmidt <schaarschmidt@biostat.uni-hannover.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Frank",
                    family = "Schaarschmidt",
                    role = c("aut", "cre"),
                    email = "schaarschmidt@biostat.uni-hannover.de")
as necessary.
Maintainer: ‘Ian Jonsen <ian.jonsen@mq.edu.au>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'reactable', 'reactable.extras'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marco Giuliano <mgiuliano.mail@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marco",
                    family = "Giuliano",
                    role = c("aut", "cre"),
                    email = "mgiuliano.mail@gmail.com")
as necessary.
Maintainer: ‘Chanseok Park <statpnu@gmail.com>’

The Description field contains
  <arXiv:2308.10150>. This work was supported by the National Research
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Alireza S. Mahani <alireza.s.mahani@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Alireza", "S."),
                      family = "Mahani",
                      role = c("aut", "cre"),
                      email = "alireza.s.mahani@gmail.com"),
               person(given = c("Mansour", "T.A."),
                      family = "Sharabiani",
                      role = "aut"))
as necessary.
Maintainer: ‘Paola Rebora <paola.rebora@unimib.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Paola", "Rebora,Agus"),
                      family = "Salim",
                      role = "aut"),
               person(given = "Marie",
                      family = "Reilly",
                      role = "aut"),
               person(given = "Paola",
                      family = "Rebora",
                      role = "cre",
                      email = "paola.rebora@unimib.it"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'bookdown', 'knitr', 'kableExtra', 'rmarkdown', 'spelling', 'Hmisc'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(bskyr)
  > 
  > test_check('bskyr')
  Error in `source_dir()`:
  ! Failed to evaluate './setup.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("bskyr")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library(vcr) at ./setup.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Leah F. South <l1.south@qut.edu.au>’

The Description field contains
  (2018) <arXiv:1809.05800>) is more robust to non-normal summary
  statistics. BSLmisspec (Frazier et al. 2019 <arXiv:1904.04551>)
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Ernesto Barrios <ebarrios@itam.mx>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ernesto", "Barrios", "based", "on", "Daniel", "Meyer's"),
                      family = "code.",
                      role = "aut"),
               person(given = "Ernesto",
                      family = "Barrios",
                      role = "cre",
                      email = "ebarrios@itam.mx"))
as necessary.
Maintainer: ‘Yanchao Liu <yanchaoliu@wayne.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yanchao",
                    family = "Liu",
                    role = c("aut", "cre"),
                    email = "yanchaoliu@wayne.edu")
as necessary.

The Description field contains
  Yanchao Liu (2022) <arXiv:2205.15263> for technical details. Source
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) bscontrol.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{opt.solver}{a character string in the set {'enum', 'enum_c', 'gurobi', 'cplex', 'lpSolve', 'greedy'} indicating the optimization solver to be used in the program. The choice of 'cplex' requires the package \code{cplexAPI}, 'gurobi' requires the package \code{gurobi}, and 'lpSolve' requires the package \code{lpSolve}. These solver options are only available in the full version at \url{https://github.com/profyliu/bsnsing/}. The default (and the best) is 'enum_c'.}
       |                                                 ^
checkRd: (-1) bscontrol.Rd:45: Lost braces; missing escapes or markup?
    45 | \item{opt.model}{a character string in the set {'gini','error'} indicating the optimization model to solve in the program. The default is 'gini'. The 'error' option is not available in the current version.}
       |                                                ^
Maintainer: ‘Jorge Sicacha-Parada <jasicachap@unal.edu.co>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jorge",
                      family = "Sicacha-Parada",
                      role = c("aut", "cre"),
                      email = "jasicachap@unal.edu.co"),
               person(given = "Edilberto",
                      family = "Cepeda-Cuervo",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Christian Roever <christian.roever@med.uni-goettingen.de>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘rmarkdown’

Packages suggested but not available for checking: 'covr', 'knitr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Deborah Burr <burr@stat.ufl.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Deborah",
                    family = "Burr",
                    role = c("aut", "cre"),
                    email = "burr@stat.ufl.edu")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Sixing Hao <s.hao3@lse.ac.uk>’

The Description field contains
  (2022)<arXiv:2201.02023>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Phillip Murray <phillip.murray18@imperial.ac.uk>’

The Description field contains
  Pakkannen (2017) <arXiv:1507.03004v4>, as well as functions to fit BSS
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools', 'kableExtra', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

Package in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Timothy Conwell <timconwell@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Timothy",
                    family = "Conwell",
                    role = c("aut", "cre"),
                    email = "timconwell@gmail.com")
as necessary.
Maintainer: ‘Zhu Wang <zwang145@uthsc.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/cancer.Rnw’
   ‘inst/doc/mcl.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'gt', 'gtsummary'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'DT', 'rmarkdown', 'DiagrammeR'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/bsvarSIGNs_vignette.Rnw’
(Is a VignetteBuilder field missing?)

Package in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/bsvars_vignette.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘vizdraws’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘ergm’

Package suggested but not available for checking: ‘Bergm’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Package suggested but not available for checking: ‘usethis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/BTYD-walkthrough.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) bubbleHMLegends.Rd:42: Lost braces; missing escapes or markup?
    42 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
checkRd: (-1) bubbleHeatmap.Rd:96: Lost braces; missing escapes or markup?
    96 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
checkRd: (-1) multiPlotInput.Rd:117: Lost braces; missing escapes or markup?
   117 | \code{unitBase}. This will be supplied to pretty function. If {sizeBreaks} is
       |                                                               ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ken Kelley <kkelley@nd.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Samantha", "F."),
                      family = "Anderson",
                      role = "aut",
                      email = "samantha.f.anderson@asu.edu"),
               person(given = "Ken",
                      family = "Kelley",
                      role = c("aut", "cre"),
                      email = "kkelley@nd.edu"))
as necessary.
Maintainer: ‘Jiwoong Kim <jwboys26@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jiwoong",
                    family = "Kim",
                    role = c("aut", "cre"),
                    email = "jwboys26atgmail.com")
as necessary.
Specified C++11: support will be removed soon
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘usethis’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2', 'spelling', 'pkgdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zhu Wang <zwang145@uthsc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhu",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "https://orcid.org/0000-0002-0773-0052"),
               person(family = "others",
                      role = "aut",
                      comment = "see COPYRIGHTS"))
as necessary.
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gprofiler2', 'shinyjqui', 'visNetwork', 'DT'

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Joseph Rigdon <jrigdon@wakehealth.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Joseph",
                    family = "Rigdon",
                    role = c("aut", "cre"),
                    email = "jrigdon@wakehealth.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

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

Packages suggested but not available for checking:
  'linkspotter', 'scagnostics', 'knitr', 'rmarkdown', 'kableExtra',
  'openintro'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marlene Marchena <marchenamarlene@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marlene",
                    family = "Marchena",
                    role = c("aut", "cre"),
                    email = "marchenamarlene@gmail.com")
as necessary.

The Description field contains
  <arXiv:1009.3977>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Lerato E Magosi <magosil86@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'Hmisc', 'rmarkdown'

Packages suggested but not available for checking: 'covr', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Philipp Ottolinger <philipp@ottolinger.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Philipp",
                    family = "Ottolinger",
                    role = c("aut", "cre"),
                    email = "philipp@ottolinger.de")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'keras', 'knitr', 'rmarkdown', 'tensorflow', 'vetiver'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘bundle-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bundle.model_fit
> ### Title: Bundle a parsnip 'model_fit' object
> ### Aliases: bundle.model_fit bundle_model_fit
> 
> ### ** Examples
> 
> ## Don't show: 
> if (rlang::is_installed("parsnip") && rlang::is_installed("xgboost")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ # fit model and bundle ------------------------------------------------
+ library(parsnip)
+ library(xgboost)
+ 
+ set.seed(1)
+ 
+ mod <-
+   boost_tree(trees = 5, mtry = 3) %>%
+   set_mode("regression") %>%
+   set_engine("xgboost") %>%
+   fit(mpg ~ ., data = mtcars)
+ 
+ mod_bundle <- bundle(mod)
+ 
+ # then, after saveRDS + readRDS or passing to a new session ----------
+ mod_unbundled <- unbundle(mod_bundle)
+ 
+ mod_unbundled_preds <- predict(mod_unbundled, new_data = mtcars)
+ ## Don't show: 
+ }) # examplesIf
> library(parsnip)
> library(xgboost)
> set.seed(1)
> mod <- boost_tree(trees = 5, mtry = 3) %>% set_mode("regression") %>% 
+     set_engine("xgboost") %>% fit(mpg ~ ., data = mtcars)
> mod_bundle <- bundle(mod)
> mod_unbundled <- unbundle(mod_bundle)
Error in xgboost::xgb.load.raw(object, as_booster = TRUE) : 
  unused argument (as_booster = TRUE)
Calls: <Anonymous> ... <Anonymous> -> unbundle -> unbundle.bundle -> <Anonymous>
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘processmapR’

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Steven Malevich <sbmalev@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘get_data_from_bursa.R’ ‘list_data_names.R’
Maintainer: ‘Pat Burns <patrick@burns-stat.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Burns",
                      family = "Statistics",
                      role = "aut"),
               person(given = "Pat",
                      family = "Burns",
                      role = "cre",
                      email = "patrick@burns-stat.com"))
as necessary.
Maintainer: ‘Pat Burns <patrick@burns-stat.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Pat",
                    family = "Burns",
                    role = c("aut", "cre"),
                    email = "patrick@burns-stat.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gnaneshwar G <gnaneshwar441@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gnaneshwar",
                    family = "G",
                    role = c("aut", "cre"),
                    email = "gnaneshwar441@gmail.com")
as necessary.
Packages required but not available: 'kableExtra', 'knitr'

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'sparklyr', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘riskRegression’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yi Zhao <zhaoyi1026@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Yi", "Zhao", "Brian", "Caffo", "<bcaffo@gmail.com>", "Joshua", "Ewen"),
                      family = "<ewen@kennedykrieger.org>",
                      role = "aut",
                      email = "ewen@kennedykrieger.org"),
               person(given = "Yi",
                      family = "Zhao",
                      role = "cre",
                      email = "zhaoyi1026@gmail.com"))
as necessary.

The Description field contains
  <arXiv:1912.13084> for details.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Fabian Krueger <Fabian.Krueger83@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Fabian",
                    family = "Krueger",
                    role = c("aut", "cre"),
                    email = "fabian.krueger83@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Author field differs from that derived from Authors@R
  Author:    ‘Franz X. Mohr [aut, cre] (0009-0003-8890-7781)’
  Authors@R: ‘Franz X. Mohr [aut, cre] (ORCiD: 0009-0003-8890-7781)’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Katharine M. Mullen <katharine.mullen@stat.ucla.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Katharine", "M."),
                    family = "Mullen",
                    role = c("aut", "cre"),
                    email = "katharine.mullen@stat.ucla.edu")
as necessary.
Malformed Description field: should contain one or more complete sentences.
Maintainer: ‘Amir Nikooienejad <amir.nikooienejad@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Amir",
                      family = "Nikooienejad",
                      role = c("aut", "cre"),
                      email = "amir.nikooienejad@gmail.com"),
               person(given = c("Valen", "E."),
                      family = "Johnson",
                      role = "ths"))
as necessary.
Specified C++11: support will be removed soon
Maintainer: ‘Seung Jun Shin <sjshin@korea.ac.kr>’

The Description field contains
  detection proposed by Shin et al. <arXiv:1812.10107>. The backward
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Carlos Biagolini-Jr.<c.biagolini@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Carlos",
                    family = "Biagolini-Jr.",
                    role = c("aut", "cre"),
                    email = "c.biagolini@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
No news entries found.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Hunyong Cho <hunyong.cho@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hunyong",
                      family = "Cho",
                      role = c("aut", "cre"),
                      email = "hunyong.cho@gmail.com"),
               person(given = "Chuwen",
                      family = "Liu",
                      role = "aut"),
               person(given = "Jinyoung",
                      family = "Park",
                      role = "aut"),
               person(given = "Di",
                      family = "Wu",
                      role = "aut"))
as necessary.
Maintainer: ‘Thomas Wieland <thomas.wieland.kit@googlemail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Wieland",
                    role = c("aut", "cre"),
                    email = "thomas.wieland.kit@googlemail.com")
as necessary.
Maintainer: ‘Mitchell Lyons <mitchell.lyons@gmail.com>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘calculate_clustering_metrics.Rd’:
    \keyword{matrix,}
    \keyword{metrics,}
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘quarto’

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gokmen Altay <altayscience@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gokmen",
                      family = "Altay",
                      role = c("aut", "cre"),
                      email = "altayscience@gmail.com"),
               person(given = "Frank",
                      family = "Emmert-Streib",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rosaria Lombardo <rosaria.lombardo@unicampania.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rosaria",
                      family = "Lombardo",
                      role = c("aut", "cre"),
                      email = "rosaria.lombardo@unicampania.it"),
               person(given = c("Eric", "J"),
                      family = "Beh",
                      role = "aut"),
               person(given = "Michel",
                      family = "van de Velden",
                      role = "aut"))
as necessary.
Packages required but not available: 'plotly', 'multichull'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Trevor Ringrose <t.j.ringrose@cranfield.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Trevor",
                    family = "Ringrose",
                    role = c("aut", "cre"),
                    email = "t.j.ringrose@cranfield.ac.uk")
as necessary.
Maintainer: ‘Junyao Jiang <jiangjunyao789@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Junyao",
                    family = "Jiang",
                    role = c("aut", "cre"),
                    email = "jiangjunyao789@163.com")
as necessary.
Package required but not available: ‘Seurat’

Package suggested but not available for checking: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Quinn N. Lathrop <quinn.lathrop@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Quinn", "N."),
                    family = "Lathrop",
                    role = c("aut", "cre"),
                    email = "quinn.lathrop@gmail.com")
as necessary.
Maintainer: ‘Alex J. Cannon <alex.cannon@canada.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Alex", "J."),
                    family = "Cannon",
                    role = c("aut", "cre"),
                    email = "alex.cannon@canada.ca")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘CADF-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Customer
> ### Title: R6 Class representing a customer.  Otherwise known as the CADF.
> ### Aliases: Customer
> 
> ### ** Examples
> 
> library(CADF)
> data("transactions")
> customer <- subset(transactions, transactions$ID == 40)
> today.study.cutoff <- max(customer$PURCHASE_DATE)
> customer.40.CADF <- Customer$new(customer, today.study.cutoff)
Error in loadNamespace(x) : there is no package called ‘jsonlite’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
CADF_to_migration_model 4.483  0.391   5.676
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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DESCRIPTION file?
Maintainer: ‘Claudio Lupi <lupi@unimol.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Claudio",
                    family = "Lupi",
                    role = c("aut", "cre"),
                    email = "lupi@unimol.it")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
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VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Felipe Campelo <fcampelo@gmail.com>’

The Description field contains
  <arxiv:1908.01720>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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Maintainer: ‘Alan Gu <alan.on.ca@gmail.com>’

No Authors@R field in DESCRIPTION.
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                    email = "alan.on.ca@gmail.com")
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VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Abbas Parchami <parchami@uk.ac.ir>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Abbas",
                    family = "Parchami",
                    role = c("aut", "cre"),
                    email = "parchami@uk.ac.ir",
                    comment = "Department of Statistics, Faculty of Mathematics and Computer, Shahid Bahonar University of Kerman, Kerman, Iran")
as necessary.
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Stephen Froehlich <stephen.froehlich@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Stephen",
                    family = "Froehlich",
                    role = c("aut", "cre"),
                    email = "stephen.froehlich@gmail.com")
as necessary.
checkRd: (-1) calcUnique.Rd:24: Lost braces
    24 | functions, and often the /code{cut()} function are relatively slow when working with tens of millions of rows or more.
       |                               ^
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
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Package required but not available: ‘ggimage’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Maintainer: ‘John Ford <JoRuFo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Stephanie",
                      family = "Lane",
                      role = c("aut", "cre")),
               person(given = "John",
                      family = "Ford",
                      role = c("aut", "cre"),
                      email = "jorufo@gmail.com"),
               person(given = "Clark",
                      family = "Jeffries",
                      role = "aut"),
               person(given = "Diana",
                      family = "Perkins",
                      role = "aut"))
as necessary.
Maintainer: ‘Anoop Shah <anoop@doctors.org.uk>’

Package CITATION file contains call(s) to old-style personList() or
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Package CITATION file contains call(s) to old-style citEntry().  Please
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Chih-Li Sung <iamdfchile@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chih-Li",
                    family = "Sung",
                    role = c("aut", "cre"),
                    email = "iamdfchile@gmail.com")
as necessary.

The Description field contains
  <arXiv:1806.01453>. This calibration method is particularly useful when
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Jan Graffelman <jan.graffelman@upc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jan",
                    family = "Graffelman",
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                    email = "jan.graffelman@upc.edu")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
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Maintainer: ‘Oyvind Langsrud <oyl@ssb.no>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
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                      family = "Langsrud",
                      role = "aut"),
               person(given = "Oyvind",
                      family = "Langsrud",
                      role = "cre",
                      email = "oyl@ssb.no"))
as necessary.
Maintainer: ‘Marius Puke <marius.puke@uni-hohenheim.de>’

Package CITATION file contains call(s) to old-style citEntry().  Please
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The Description field contains
  <arXiv:2203.04065>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) calibration_bands.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{y}{response variable (in {0,1}).}
       |                                ^
Packages required but not available:
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Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Robin K. S. Hankin <hankin.robin@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
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Maintainer: ‘Dominik Heider <heiderd@mathematik.uni-marburg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Johanna",
                      family = "Schwarz",
                      role = "aut"),
               person(given = "Dominik",
                      family = "Heider",
                      role = c("aut", "cre"),
                      email = "heiderd@mathematik.uni-marburg.de"))
as necessary.
Package required but not available: ‘kableExtra’

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VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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VignetteBuilder package required for checking but not installed: ‘knitr’
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Maintainer: ‘Henrik Bengtsson <henrikb@braju.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
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VignetteBuilder package required for checking but not installed: ‘knitr’
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Package required but not available: ‘DT’

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VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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VignetteBuilder package required for checking but not installed: ‘knitr’
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checkRd: (-1) Recording.Rd:112: Lost braces; missing escapes or markup?
   112 | Stop recording images with {camcorder}.
       |                            ^
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VignetteBuilder package required for checking but not installed: ‘knitr’
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VignetteBuilder package required for checking but not installed: ‘knitr’
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Maintainer: ‘Lukas Lundstrom <lukas.rokka@gmail.com>’

Found the following (possibly) invalid file URI:
  URI: CONDUCT.md
    From: README.md
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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VignetteBuilder package required for checking but not installed: ‘knitr’
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VignetteBuilder package required for checking but not installed: ‘knitr’
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Maintainer: ‘Audrey Q. Fu <audreyqyfu@gmail.com>’

No Authors@R field in DESCRIPTION.
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  Authors@R: c(person(given = c("Audrey", "Qiuyan"),
                      family = "Fu",
                      role = "aut"),
               person(given = "Xiaoyue",
                      family = "Wang",
                      role = "aut"),
               person(given = c("Audrey", "Q."),
                      family = "Fu",
                      role = "cre",
                      email = "audreyqyfu@gmail.com"))
as necessary.
Maintainer: ‘Michal Burdukiewicz <michalburdukiewicz@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
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Package required but not available: ‘devtools’

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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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  'plotly', 'tidyverse', 'DT', 'knitr', 'quarto'

VignetteBuilder package required for checking but not installed: ‘quarto’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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DESCRIPTION file?
Maintainer: ‘Yuchao Jiang <yuchaoj@email.unc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yuchao",
                      family = "Jiang",
                      role = c("aut", "cre"),
                      email = "yuchaoj@email.unc.edu"),
               person(given = c("Nancy", "R."),
                      family = "Zhang",
                      role = "aut"))
as necessary.
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VignetteBuilder package required for checking but not installed: ‘knitr’
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Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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VignetteBuilder package required for checking but not installed: ‘knitr’
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DESCRIPTION file?
Maintainer: ‘John T. Buynak <jbuynak94@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("John", "T."),
                    family = "Buynak",
                    role = c("aut", "cre"),
                    email = "jbuynak94@gmail.com")
as necessary.
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VignetteBuilder package required for checking but not installed: ‘knitr’
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Maintainer: ‘Joel Barnes <j@barnzilla.ca>’

Package CITATION file contains call(s) to old-style citEntry().  Please
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'library' or 'require' call not declared from: ‘deSolve’
Packages required but not available:
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Maintainer: ‘Gaurav Sood <gsood07@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
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Problems with news in ‘NEWS.md’:
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    captr .1.4
    captr .1.3
    captr .1.2
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Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘do_la.Rd’ ‘linalg.Rd’ ‘scale_matrix.Rd’ ‘solve.caracas_symbol.Rd’
    ‘solve_lin.Rd’
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Maintainer: ‘Duncan Lee <Duncan.Lee@glasgow.ac.uk>’

No Authors@R field in DESCRIPTION.
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  Authors@R: person(given = "Duncan",
                    family = "Lee",
                    role = c("aut", "cre"),
                    email = "duncan.lee@glasgow.ac.uk")
as necessary.
Maintainer: ‘Duncan Lee <Duncan.Lee@glasgow.ac.uk>’

No Authors@R field in DESCRIPTION.
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  Authors@R: person(given = "Duncan",
                    family = "Lee",
                    role = c("aut", "cre"),
                    email = "duncan.lee@glasgow.ac.uk")
as necessary.
Package required but not available: ‘mapview’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Duncan Lee <Duncan.Lee@glasgow.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Duncan",
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "duncan.lee@glasgow.ac.uk"),
               person(given = "Alastair",
                      family = "Rushworth",
                      role = "aut"),
               person(given = "Gary",
                      family = "Napier",
                      role = "aut"),
               person(given = "William",
                      family = "Pettersson",
                      role = "aut"))
as necessary.
Package required but not available: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Maintainer: ‘Oleg Nenadic <onenadi@uni-goettingen.de>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) plot.ca.rd:53: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) plot.mjca.rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) fitweibull.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'langevitour', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘cosinor-constructor.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Korbinian Strimmer <strimmerlab@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Verena",
                      family = "Zuber",
                      role = "aut"),
               person(given = "Korbinian",
                      family = "Strimmer.",
                      role = "aut"),
               person(given = "Korbinian",
                      family = "Strimmer",
                      role = "cre",
                      email = "strimmerlab@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'lintr', 'rmarkdown', 'spelling', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'gam', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'ecospat', 'mapview'

Packages suggested but not available for checking:
  'roxyglobals', 'covr', 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Hyungsuk Tak <hyungsuk.tak@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hyungsuk",
                      family = "Tak",
                      role = c("aut", "cre"),
                      email = "hyungsuk.tak@gmail.com"),
               person(given = "Henghsiu",
                      family = "Tsai",
                      role = "aut"),
               person(given = "Kisung",
                      family = "You",
                      role = "aut"))
as necessary.
checkRd: (-1) build_for_cran.Rd:13: Lost braces
    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
Maintainer: ‘Stéphane Laurent <laurent_step@outlook.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Stéphane",
                    family = "Laurent",
                    role = c("aut", "cre"),
                    email = "laurent_step@outlook.fr")
as necessary.
Maintainer: ‘Ziyi Li <zli16@mdanderson.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ziyi",
                    family = "Li",
                    role = c("aut", "cre"),
                    email = "zli16@mdanderson.org")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rgl'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Thomas Welchowski <welchow@imbie.meb.uni-bonn.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Welchowski",
                    role = c("aut", "cre"),
                    email = "welchow@imbie.meb.uni-bonn.de")
as necessary.

The Description field contains
  <arXiv:1802.08178>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rnaturalearthhires', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
File ‘cartographer/libs/cartographer.so’:
  Found non-API call to R: ‘PRVALUE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yaofang Hu <yaofangh@smu.edu>’

The Description field contains
  Wang (2022) <arXiv:2306.15616>.  In addition to CASCORE, this package
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rms’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rich Nielsen <rnielsen@mit.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Rich",
                    family = "Nielsen",
                    role = c("aut", "cre"),
                    email = "rnielsen@mit.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'badger'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running examples in ‘casimir-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute_propensity_scores
> ### Title: Compute inverse propensity scores
> ### Aliases: compute_propensity_scores
> 
> ### ** Examples
> 
> 
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'mapview', 'rmarkdown', 'tmap'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘sparklyr’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yuqing Pan <yuqing.pan@stat.fsu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yuqing",
                      family = "Pan",
                      role = c("aut", "cre"),
                      email = "yuqing.pan@stat.fsu.edu"),
               person(given = "Qing",
                      family = "Mai",
                      role = "aut",
                      email = "mai@stat.fsu.edu"),
               person(given = "Xin",
                      family = "Zhang",
                      role = "aut",
                      email = "henry@stat.fsu.edu"))
as necessary.

The Description field contains
  (2018) <arXiv:1805.04421>. The low-dimensional covariates and the
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Masami Saga <msaga@mtb.biglobe.ne.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("The", "Institute", "of", "Statistical"),
                      family = "Mathematics",
                      role = "aut"),
               person(given = "Masami",
                      family = "Saga",
                      role = "cre",
                      email = "msaga@mtb.biglobe.ne.jp"))
as necessary.
Maintainer: ‘Charles J. Geyer <charlie@stat.umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alan",
                      family = "Agesti",
                      role = "aut",
                      email = "aa@stat.ufl.edu"),
               person(given = c("Charles", "J."),
                      family = "Geyer",
                      role = "cre",
                      email = "charlie@stat.umn.edu"))
as necessary.
Packages suggested but not available for checking: 'knitr', 'rms'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/altbin-teratology.Rnw’
   ‘inst/doc/binary-unemployment.Rnw’
   ‘inst/doc/binary-vaso.Rnw’
   ‘inst/doc/count-children.Rnw’
   ‘inst/doc/count-encephalitis.Rnw’
   ‘inst/doc/count-insolvency.Rnw’
   ‘inst/doc/count-medcare.Rnw’
   ‘inst/doc/loglinear-birth.Rnw’
   ‘inst/doc/loglinear-leukoplakia.Rnw’
   ‘inst/doc/modbin-dust.Rnw’
   ‘inst/doc/modbin-foodstamp.Rnw’
   ‘inst/doc/modbin-unemployment1.Rnw’
   ‘inst/doc/modbin-unemployment2.Rnw’
   ‘inst/doc/multinomial-addiction1.Rnw’
   ‘inst/doc/multinomial-addiction2.Rnw’
   ‘inst/doc/multinomial-party1.Rnw’
   ‘inst/doc/multinomial-party2.Rnw’
   ‘inst/doc/multinomial-travel.Rnw’
   ‘inst/doc/multivariate-birth1.Rnw’
   ‘inst/doc/multivariate-birth2.Rnw’
   ‘inst/doc/multivariate-knee.Rnw’
   ‘inst/doc/ordinal-arthritis.Rnw’
   ‘inst/doc/ordinal-knee1.Rnw’
   ‘inst/doc/ordinal-knee2.Rnw’
   ‘inst/doc/ordinal-retinopathy1.Rnw’
   ‘inst/doc/ordinal-retinopathy2.Rnw’
   ‘inst/doc/prediction-medcare.Rnw’
   ‘inst/doc/random-aids.Rnw’
   ‘inst/doc/random-betablocker.Rnw’
   ‘inst/doc/random-knee1.Rnw’
   ‘inst/doc/random-knee2.Rnw’
   ‘inst/doc/random-knee3.Rnw’
   ‘inst/doc/semiparametric-addiction.Rnw’
   ‘inst/doc/semiparametric-children.Rnw’
   ‘inst/doc/semiparametric-dust.Rnw’
   ‘inst/doc/semiparametric-unemployment.Rnw’
   ‘inst/doc/tree-dust.Rnw’
   ‘inst/doc/tree-unemployment.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ruben H. Roa-Ureta <ruben.roa.ureta@mail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Ruben", "H."),
                    family = "Roa-Ureta",
                    role = c("aut", "cre"),
                    email = "ruben.roa.ureta@mail.com")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Juraj Szitas <szitas.juraj13@gmail.com>’

The Description field contains
  Hadad, Athey, Wager (2019) <arXiv:1908.09874>, particularly their mean,
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘nl zhang <setseed2016@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "nl",
                    family = "zhang",
                    role = c("aut", "cre"),
                    email = "setseed2016@gmail.com")
as necessary.
Maintainer: ‘Nick Williams <ntwilliams.personal@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nick",
                    family = "Williams",
                    role = c("aut", "cre"),
                    email = "ntwilliams.personal@gmail.com")
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Adrien Taudiere <adrien.taudiere@tutanota.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'tidyverse', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) catmapdata.Rd:9-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:20-21: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Fernando Tusell <fernando.tusell@ehu.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ported", "to", "R", "by", "Ted"),
                      family = "Harding",
                      role = "aut"),
               person(given = c("Fernando", "Tusell.", "Original", "by", "Joseph", "L."),
                      family = "Schafer.",
                      role = "aut",
                      email = "jls@stat.psu.edu"),
               person(given = "Fernando",
                      family = "Tusell",
                      role = "cre",
                      email = "fernando.tusell@ehu.es"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'tidyverse', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Cheng Hua <chuabest@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Magis",
                      role = "aut",
                      comment = "U Liege, Belgium"),
               person(given = "Gilles",
                      family = "Raiche",
                      role = "aut",
                      comment = "UQAM, Canada"),
               person(given = c("Juan", "Ramon"),
                      family = "Barrada",
                      role = "aut",
                      comment = "U Zaragoza, Spain"),
               person(given = "Cheng",
                      family = "Hua",
                      role = "cre",
                      email = "chuabest@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zhicheng Du<dgdzc@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhicheng",
                      family = "Du",
                      role = c("aut", "cre"),
                      email = "dgdzc@hotmail.com"),
               person(given = "Yuantao",
                      family = "Hao",
                      role = "aut"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘CATT.Rd’:
    \keyword{Cochran-Armitage; Trend Test}
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘DiagrammeR’

Packages suggested but not available for checking:
  'knitr', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown', 'tidyverse', 'ggalt', 'DT',
  'Hmisc', 'hrbrthemes'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'PSweight', 'knitr'

Packages suggested but not available for checking: 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
Packages suggested but not available for checking:
  'Hmisc', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/Using_causaldrf.Rnw’
(Is a VignetteBuilder field missing?)

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kevin Quinn <kmq@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Adam",
                      family = "Glynn",
                      role = "aut",
                      email = "adam.glynn@emory.edu"),
               person(given = "Kevin",
                      family = "Quinn",
                      role = c("aut", "cre"),
                      email = "kmq@umich.edu"))
as necessary.
Package required but not available: ‘gam’

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Fiammetta Menchetti <fiammetta.menchetti@gmail.com>’

The Description field contains
  (MBSTS) as described in Menchetti & Bojinov (2020) <arXiv:2006.12269>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) as.mbsts.Rd:71: Lost braces; missing escapes or markup?
    71 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
checkRd: (-1) mcmc.Rd:61: Lost braces; missing escapes or markup?
    61 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘SuperLearner’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘causal-model.R’ ‘check-linearity.R’ ‘deprecated.R’
    ‘translation-modules.R’ ‘utils.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Eric Dunipace <edunipace@mail.harvard.edu>’

The Description field contains
  Dunipace, Eric (2021) <arXiv:2109.01991>.  The package will build the
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rkeops', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cotOOP.R’ ‘utils.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Found the following HTML validation problems:
causalOT.html:1690:1 (Measure_-class.Rd:60): Warning: <a> anchor "method-Measure-detach" already defined
causalOT.html:1706:1 (Measure_-class.Rd:70): Warning: <a> anchor "method-Measure-get_weight_parameters" already defined
causalOT.html:1803:1 (Measure_-class.Rd:137): Warning: <a> anchor "method-Measure-clone" already defined
causalOT.html:2452:1 (OTProblem_-class.Rd:50): Warning: <a> anchor "method-OTProblem-add" already defined
causalOT.html:2481:1 (OTProblem_-class.Rd:67): Warning: <a> anchor "method-OTProblem-subtract" already defined
causalOT.html:2510:1 (OTProblem_-class.Rd:84): Warning: <a> anchor "method-OTProblem-multiply" already defined
causalOT.html:2539:1 (OTProblem_-class.Rd:101): Warning: <a> anchor "method-OTProblem-divide" already defined
causalOT.html:2637:1 (OTProblem_-class.Rd:159): Warning: <a> anchor "method-OTProblem-setup_arguments" already defined
causalOT.html:2700:1 (OTProblem_-class.Rd:207): Warning: <a> anchor "method-OTProblem-solve" already defined
causalOT.html:2752:1 (OTProblem_-class.Rd:247): Warning: <a> anchor "method-OTProblem-choose_hyperparameters" already defined
causalOT.html:2789:1 (OTProblem_-class.Rd:272): Warning: <a> anchor "method-OTProblem-info" already defined
causalOT.html:2826:1 (OTProblem_-class.Rd:290): Warning: <a> anchor "method-OTProblem-clone" already defined
Package required but not available: ‘rlist’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Packages suggested but not available for checking: 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Matthew Blackwell <mblackwell@gov.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Matthew",
                    family = "Blackwell",
                    role = c("aut", "cre"),
                    email = "mblackwell@gov.harvard.edu.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘SuperLearner’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'pkgdown', 'PSweight', 'rmarkdown', 'roxygen2',
  'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Giovanna Capizzi <giovanna.capizzi@unipd.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Giovanna",
                      family = "Capizzi",
                      role = c("aut", "cre"),
                      email = "giovanna.capizzi@unipd.it"),
               person(given = "Guido",
                      family = "Masarotto",
                      role = "aut"))
as necessary.
Maintainer: ‘Rosaria Lombardo  <rosaria.lombardo@unicampania.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rosaria",
                      family = "Lombardo",
                      role = c("aut", "cre"),
                      email = "rosaria.lombardo@unicampania.it"),
               person(given = c("Eric", "J"),
                      family = "Beh",
                      role = "aut"))
as necessary.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Zhongheng Zhang <zh_zhang1984@zju.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhongheng",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "zh_zhang1984@zju.edu.cn"),
               person(given = c("Sir", "Run", "Run", "Shaw"),
                      family = "hospital",
                      role = "aut"),
               person(given = c("Zhejiang", "university", "school", "of"),
                      family = "medicine",
                      role = "aut"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘CBCgrps2.6-package.Rd’:
    \keyword{ bivariate analysis; statisitcal descript [TRUNCATED]
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Dan Dalthorp <ddalthorp@protonmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dan",
                    family = "Dalthorp",
                    role = c("aut", "cre"),
                    email = "ddalthorp@protonmail.com")
as necessary.

The Description field contains
  (2013) <arXiv:1303.5990>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘David Watson <david.s.watson11@gmail.com>’

The Description field contains
  details, see Watson & Silva (2022) <arXiv:2205.05715>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Shouri Hu <e0054325@u.nus.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Hock", "Peng"),
                      family = "Chan",
                      role = "aut"),
               person(given = "Shouri",
                      family = "Hu",
                      role = c("aut", "cre"),
                      email = "e0054325@u.nus.edu"))
as necessary.

The Description field contains
  and Shouri Hu (2018) <arXiv:1805.11793>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/ccaPP-intro.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sébastien Déjean <sebastien.dejean@math.univ-toulouse.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ignacio",
                      family = "González",
                      role = "aut"),
               person(given = "Sébastien",
                      family = "Déjean",
                      role = c("aut", "cre"),
                      email = "sebastien.dejean@math.univ-toulouse.fr"))
as necessary.
Maintainer: ‘David J. Marchette <dmarchette@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("David", "J."),
                    family = "Marchette",
                    role = c("aut", "cre"),
                    email = "dmarchette@gmail.com")
as necessary.
Maintainer: ‘Solt Kovacs <ccda@caesar.elte.hu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Solt",
                      family = "Kovacs",
                      role = c("aut", "cre"),
                      email = "ccda@caesar.elte.hu"),
               person(given = "Jozsef",
                      family = "Kovacs",
                      role = "aut"),
               person(given = "Peter",
                      family = "Tanos",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'countcolors', 'devtools', 'DT', 'knitr', 'prettydoc', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Andreas Anastasiou <anastasiou.andreas@ucy.ac.cy>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael B. Sohn <msohn@mail.med.upenn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Michael", "B."),
                    family = "Sohn",
                    role = c("aut", "cre"),
                    email = "msohn@mail.med.upenn.edu")
as necessary.
Maintainer: ‘Garrett M. Dancik <dancikg@easternct.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Garrett", "M."),
                      family = "Dancik",
                      role = c("aut", "cre"),
                      email = "dancikg@easternct.edu"),
               person(given = "Yuanbin",
                      family = "Ru",
                      role = "aut"))
as necessary.
Package required but not available: ‘keyring’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Uwe Menzel <uwemenzel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Uwe",
                    family = "Menzel",
                    role = c("aut", "cre"),
                    email = "uwemenzel@gmail.com")
as necessary.
Packages required but not available: 'ufs', 'xlsx'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘W.John Braun <john.braun@ubc.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "W.J.",
                      family = "Braun",
                      role = "aut"),
               person(given = "W.John",
                      family = "Braun",
                      role = "cre",
                      email = "john.braun@ubc.ca"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Abhibhav Sharma <mail.abhibhav@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Abhibhav",
                    family = "Sharma",
                    role = c("aut", "cre"),
                    email = "mail.abhibhav@gmail.com")
as necessary.
Maintainer: ‘Yonghui Dong <yonghui.dong@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yonghui",
                    family = "Dong",
                    role = c("aut", "cre"),
                    email = "yonghui.dong@gmail.com")
as necessary.
Packages required but not available: 'plotly', 'DT', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'yaml'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘tinytest.R’ [3s/4s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("cdata")
  + }
  Loading required package: wrapr
  
  Attaching package: 'wrapr'
  
  The following object is masked from 'package:base':
  
      grepv
  
  
  test_RowColOps.R..............    0 tests    
  test_RowColOps.R..............    3 tests [0;32mOK[0m [0;34m0.3s[0m
  
  test_XForm.R..................    0 tests    
  test_XForm.R..................    8 tests [0;32mOK[0m [0;34m0.9s[0m
  
  test_check.R..................    0 tests    
  test_check.R..................    1 tests [0;32mOK[0m [0;34m0.1s[0m
  
  test_checks_2.R...............    0 tests    
  test_checks_2.R...............    9 tests [0;32mOK[0m [0;34m0.2s[0m
  
  test_chicks.R.................    0 tests    
  test_chicks.R.................    1 tests [0;32mOK[0m [0;36m91ms[0m
  Loading required package: rquery
  
  test_complex_example.R........    0 tests    
  test_complex_example.R........    0 tests    
  test_complex_example.R........    0 tests    
  test_complex_example.R........    2 tests [0;32mOK[0m [0;34m0.4s[0m
  
  test_composite_control_keys.R.    0 tests    
  test_composite_control_keys.R.    4 tests [0;32mOK[0m [0;36m53ms[0m
  
  test_composite_control_keys_db.R    0 tests    
  test_composite_control_keys_db.R    4 tests [0;32mOK[0m [0;34m0.5s[0m
  
  test_dates.R..................    0 tests    
  test_dates.R..................   10 tests [0;32mOK[0m [0;36m55ms[0m
  
  test_encode.R.................    0 tests    
  test_encode.R.................    4 tests [0;32mOK[0m 
  test_encode.R.................    4 tests [0;32mOK[0m Error in loadNamespace(x) : there is no package called 'yaml'
  Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Problems with news in ‘NEWS.md’:
No news entries found.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘cdfquantreg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cdfqrFamily
> ### Title: Overview of the family of distributions
> ### Aliases: cdfqrFamily
> 
> ### ** Examples
> 
> cdfqrFamily()
Overview cdfquantreg distributions:Error in loadNamespace(x) : there is no package called ‘knitr’
Calls: cdfqrFamily ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mathieu Vrac <mathieu.vrac@lsce.ipsl.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mathieu",
                      family = "Vrac",
                      role = c("aut", "cre"),
                      email = "mathieu.vrac@lsce.ipsl.fr"),
               person(given = "Paul-Antoine",
                      family = "Michelangeli",
                      role = "aut",
                      email = "pam@climpact.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Alicja Wolny-Dominiak <woali@ue.katowice.pl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Peter",
                      family = "Adamic",
                      role = "aut"),
               person(given = "Alicja",
                      family = "Wolny-Dominiak",
                      role = c("aut", "cre"),
                      email = "woali@ue.katowice.pl"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'SqlRender', 'CirceR', 'rJava', 'covr', 'knitr', 'rmarkdown',
  'DatabaseConnector'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) tblGroup.Rd:21: height/width attributes should be in pixels
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Philippe Massicotte <pm@bios.au.dk>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Norm Matloff <normmatloff@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Norm",
                      family = "Matloff",
                      role = c("aut", "cre"),
                      email = "normmatloff@gmail.com"),
               person(given = "Vincent",
                      family = "Yang",
                      role = "aut",
                      email = "vinyang@ucdavis.edu"),
               person(given = "Harrison",
                      family = "Nguyen",
                      role = "aut",
                      email = "hhnguy@ucdavis.edu"))
as necessary.
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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Maintainer: ‘Emanuele Bevacqua <emanuele.bevacqua@uni-graz.at>’

Package CITATION file contains call(s) to old-style personList() or
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Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
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Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘atp_plot.Rd’ ‘bioscope_plot.Rd’ ‘energetics_lme_summary.Rd’
    ‘energetics_ols_summary.Rd’ ‘fit_lme.Rd’ ‘get_energetics.Rd’
    ‘get_energetics_summary.Rd’ ‘get_rate_summary.Rd’
    ‘make_bioscope_plot.Rd’ ‘normalize.Rd’ ‘partition_data.Rd’
    ‘pipelines.r’ ‘rate_plot.R’ ‘rate_plot.Rd’ ‘rates_lme_summary.Rd’
    ‘read_data.Rd’
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Package required but not available: ‘mixtools’

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VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
Package required but not available: ‘ensembldb’

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  'knitr', 'plotly', 'rmarkdown'

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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Maintainer: ‘David Molnar <dmolnar100@icloud.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Molnar",
                    role = c("aut", "cre"),
                    email = "dmolnar100@icloud.com")
as necessary.
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Maintainer: ‘Katharine M. Mullen <katharine.mullen@stat.ucla.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Katharine", "M."),
                      family = "Mullen",
                      role = c("aut", "cre"),
                      email = "katharine.mullen@stat.ucla.edu"),
               person(given = "Michael",
                      family = "Halter",
                      role = "aut"),
               person(given = "John",
                      family = "Lu",
                      role = "aut"),
               person(given = "Nathan",
                      family = "Dodder",
                      role = "aut"))
as necessary.
Cannot process vignettes
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Maintainer: ‘Andre Fujita <andrefujita@usp.br>’

The Description field contains
  structures (Relvas C. & Fujita A., (2020) <arXiv:2004.02333>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Sy Han (Steven) Chiou <schiou@hsph.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jing",
                      family = "Qian",
                      role = "aut"),
               person(given = c("Sy", "Han"),
                      family = "Chiou",
                      role = "aut",
                      comment = "Steven"),
               person(given = c("Sy", "Han"),
                      family = "Chiou",
                      role = "cre",
                      email = "schiou@hsph.harvard.edu",
                      comment = "Steven"))
as necessary.
Cannot process vignettes
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Yan Li <YanLi_stats@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yan",
                      family = "Li",
                      role = c("aut", "cre"),
                      email = "yanli_stats@hotmail.com"),
               person(given = "Yang",
                      family = "Li",
                      role = "aut"),
               person(given = "Yichen",
                      family = "Qin",
                      role = "aut"),
               person(given = "Jun",
                      family = "yan",
                      role = "aut"))
as necessary.
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Maintainer: ‘Arne Henningsen <arne.henningsen@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Arne",
                    family = "Henningsen",
                    role = c("aut", "cre"),
                    email = "arne.henningsen@gmail.com")
as necessary.
Maintainer: ‘Alejandro Ordonez <ordonezjosealejandro@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alejandro",
                      family = "Ordonez",
                      role = c("aut", "cre"),
                      email = "ordonezjosealejandro@gmail.com"),
               person(given = c("Christian", "E."),
                      family = "Galarza",
                      role = "aut"),
               person(given = c("Victor", "H."),
                      family = "Lachos",
                      role = "aut"))
as necessary.
Cannot process vignettes
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) call_api_once.Rd:36: Lost braces
    36 | A code{data.frame} with the requested variables at the requested
       |       ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
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Maintainer: ‘Mahdi Jalili <m_jalili@farabi.tums.ac.ir>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mahdi",
                    family = "Jalili",
                    role = c("aut", "cre"),
                    email = "m_jalili@farabi.tums.ac.ir")
as necessary.
checkRd: (-1) centroid.Rd:22: Lost braces; missing escapes or markup?
    22 | Centroid value C_{cen}(v) for node v defined as:
       |                  ^
checkRd: (-1) clusterrank.Rd:23: Lost braces; missing escapes or markup?
    23 | where the term f(c_{i}) accounts for the effect of i's local clustering and the term '+1' results from the contribution of \eqn{j}{j} itself. \cr
       |                    ^
Maintainer: ‘Duy Nghia Pham <nghiapham@yandex.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Benoit Liquet <b.liquet@uq.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tim",
                      family = "Benham",
                      role = "aut"),
               person(given = "Qibin",
                      family = "Duan",
                      role = "aut"),
               person(given = c("Dirk", "P."),
                      family = "Kroese",
                      role = "aut"),
               person(given = "Benoit",
                      family = "Liquet",
                      role = c("aut", "cre"),
                      email = "b.liquet@uq.edu.au"))
as necessary.
Maintainer: ‘Mohit Dayal <mohitdayal2000@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mohit",
                    family = "Dayal",
                    role = c("aut", "cre"),
                    email = "mohitdayal2000@gmail.com")
as necessary.
Cannot process vignettes
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  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ce-hg.R’ ‘ce-mean.R’ ‘ce-prepdata.R’ ‘ce-quantiles.R’ ‘ce-uccs.R’
    ‘get-survey-files.R’ ‘read-expd.R’ ‘read-fmld.R’ ‘read-fmli.R’
    ‘read-mtbi.R’ ‘recode-ce-variables.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
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Maintainer: ‘Yijian Huang <yhuang5@emory.edu>’

No Authors@R field in DESCRIPTION.
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  Authors@R: person(given = "Yijian",
                    family = "Huang",
                    role = c("aut", "cre"),
                    email = "yhuang5@emory.edu")
as necessary.
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VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |   ^
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |          ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
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Cannot process vignettes
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  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mengying Zhang <zhangmengying@hrbmu.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Mengying", "Zhang,Yongsheng", "Li,Juan", "Xu*,Xia"),
                      family = "Li*",
                      role = "aut"),
               person(given = "Mengying",
                      family = "Zhang",
                      role = "cre",
                      email = "zhangmengying@hrbmu.edu.cn"))
as necessary.
Cannot process vignettes
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Packages required but not available:
  'DT', 'colourpicker', 'flextable', 'shinyjqui', 'plotly',
  'shinyTree', 'sortable'

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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'colourpicker', 'flextable', 'shinyjqui', 'plotly', 'shinyTree',
  'sortable'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'plotly', 'shinyjqui', 'sortable'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'colourpicker', 'DT', 'plotly', 'shinyjqui', 'sortable'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Diogo Ferrari <diogoferrari@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘James Balamuta <balamut2@illinois.edu>’

Found the following (possibly) invalid file URI:
  URI: RColorBrewer
    From: README.md

The Description field contains
  (2015) "Good Colour Maps: How to Design Them" <arXiv:1509.03700> at the
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Hmisc’

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VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Brett Moore <Brett.Moore@nrcan-rncan.gc.ca>’

The BugReports field in DESCRIPTION has
  https://github.com/cffdrs/cffdrs_r/issues/new/choose
which should likely be
  https://github.com/cffdrs/cffdrs_r/issues/new/choose/issues
instead.
Package required but not available: ‘yaml’

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  'knitr', 'rmarkdown', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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  'bookdown', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Erick Verleye <erve3705@colorado.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘rlist’

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ahmadou Dicko <mail@ahmadoudicko.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "file",
                      family = "inst/AUTHORS",
                      role = "aut"),
               person(given = "Ahmadou",
                      family = "Dicko",
                      role = "cre",
                      email = "mail@ahmadoudicko.com"))
as necessary.
Maintainer: ‘Yu-chia Chang <curare7177@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Yuan-chin", "I."),
                      family = "Chang",
                      role = "aut"),
               person(given = "Yu-chia",
                      family = "Chang",
                      role = c("aut", "cre"),
                      email = "curare7177@gmail.com"),
               person(given = "Ling-wan",
                      family = "Chen",
                      role = "aut"))
as necessary.
Malformed Title field: should not end in a period.
Maintainer: ‘LI Wu <liwu@staff.shu.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "LI",
                    family = "Wu",
                    role = c("aut", "cre"),
                    email = "liwu@staff.shu.edu.cn")
as necessary.
Cannot process vignettes
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  'covr', 'rmarkdown', 'knitr'

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Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
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Maintainer: ‘Arvid Sjolander <arvid.sjolander@ki.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Arvid",
                    family = "Sjolander",
                    role = c("aut", "cre"),
                    email = "arvid.sjolander@ki.se")
as necessary.
Package required but not available: ‘MESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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  'knitr', 'rmarkdown', 'iglu', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘cgmguru-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: detect_all_events
> ### Title: Detect All Glycemic Events
> ### Aliases: detect_all_events
> 
> ### ** Examples
> 
> # Load sample data
> library(iglu)
Error in library(iglu) : there is no package called ‘iglu’
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tidyverse’

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VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Shan Ba <shanbatr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Shan",
                      family = "Ba",
                      role = c("aut", "cre"),
                      email = "shanbatr@gmail.com"),
               person(given = c("V.", "Roshan"),
                      family = "Joseph",
                      role = "aut"))
as necessary.
Packages required but not available: 'Hmisc', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Carl Witthoft <cellocgw@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Carl",
                    family = "Witthoft",
                    role = c("aut", "cre"),
                    email = "cellocgw@gmail.com")
as necessary.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Haotian Xu <haotian.xu@uclouvain.be>’

The Description field contains
  <arXiv:2006.03283>; 2) univariate polynomials:
  <doi:10.1214/20-AOS1953>, <arXiv:2101.05477>, <arXiv:2110.06450>; 6)
  high-dimensional linear regression models: <arXiv:2010.10410>,
  <arXiv:2207.12453>; 7) high-dimensional vector autoregressive models:
  <arXiv:1909.06359>; 8) high-dimensional self exciting point processes:
  <arXiv:2006.03572>; 9) dependent dynamic nonparametric random dot
  product graphs: <arXiv:1911.07494>; 10) univariate mean against
  adversarial attacks: <arXiv:2105.10417>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
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  'knitr', 'DiagrammeR', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) Hausdorff.dist.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{vec1}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) Hausdorff.dist.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{vec2}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) online.univar.multi.Rd:47-57: Lost braces
    47 | online.univar.one2 = function(y_vec, gamma, tau_gamma, ...){
       |                                                            ^
checkRd: (-1) online.univar.multi.Rd:50-55: Lost braces
    50 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:71-89: Lost braces
    71 | online.univar.one3 = function(y_vec, tau_vec, ...){
       |                                                   ^
checkRd: (-1) online.univar.multi.Rd:72-74: Lost braces
    72 |   if(length(y_vec) != length(tau_vec)){
       |                                       ^
checkRd: (-1) online.univar.multi.Rd:77-87: Lost braces
    77 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:81-86: Lost braces
    81 |     while(j < J & FLAG == 0){
       |                             ^
Running examples in ‘changepoints-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: WBS.univar
> ### Title: Wild binary segmentation for univariate mean change points
> ###   detection.
> ### Aliases: WBS.univar
> 
> ### ** Examples
> 
> set.seed(0)
> cpt_true = c(20, 50, 170)
> y = rnorm(300) + c(rep(0,20),rep(2,30),rep(0,120),rep(2,130))
> intervals = WBS.intervals(M = 300, lower = 1, upper = length(y))
> temp = WBS.univar(y, 1, length(y), intervals$Alpha, intervals$Beta, delta = 5)
> plot.ts(y)
> points(x = tail(temp$S[order(temp$Dval)],4),
+        y = y[tail(temp$S[order(temp$Dval)],4)], col = "red")
> WBS_result = thresholdBS(temp, tau = 4)
> print(WBS_result$BS_tree, "value")
                                      levelName     value
1 Binary Segmentation Tree Trimmed with tau = 4        NA
2  °--N170                                      15.667978
3      °--N50                                    9.957747
4          °--N20                                7.301167
> plot(WBS_result$BS_tree)
Error in plot.Node(WBS_result$BS_tree) : 
  Package "DiagrammeR" is required to plot a `data.tree::Node`object. Please install it.
Calls: plot -> plot.Node
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Davide Altomare <davide.altomare@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Davide",
                    family = "Altomare",
                    role = c("aut", "cre"),
                    email = "davide.altomare@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DatabaseConnector', 'FeatureExtraction', 'SqlRender',
  'ResultModelManager'

Packages suggested but not available for checking:
  'devtools', 'kableExtra', 'knitr', 'rmarkdown',
  'OhdsiShinyAppBuilder'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Found the following HTML validation problems:
charlatan.html:21530:1 (PhoneNumberProvider_no_NO.Rd:60): Warning: <a> anchor "method-PhoneNumberProvider_nn_NO-clone" already defined
checkRd: (-1) cql.Rd:28: Lost braces; missing escapes or markup?
    28 | {X} \code{<x_var>, <(x_facet)>}: \tab\tab\tab\tab  X-axis variable. May include a second categorical\cr
       | ^
checkRd: (-1) cql.Rd:30: Lost braces; missing escapes or markup?
    30 | {Y} \code{<y_var>}: \tab\tab\tab\tab Y-axis variable. *Not used for \code{hist}.\cr
       | ^
checkRd: (-1) cql.Rd:38: Lost braces; missing escapes or markup?
    38 | {Y_label} \code{'<ylab>'}: \tab\tab\tab\tab  Y-axis custom label. Defaults to <y_var>\cr
       | ^
checkRd: (-1) cql.Rd:39: Lost braces; missing escapes or markup?
    39 | {Legend} \code{'<legend>'}: \tab\tab\tab\tab  Legend custom label. Defaults to <x_category>\cr
       | ^
checkRd: (-1) cql.Rd:40: Lost braces; missing escapes or markup?
    40 | {Colorset} \code{'<clist>'}: \tab\tab\tab\tab  Custom set of colors for <x_category> levels.\cr
       | ^
checkRd: (-1) cql.Rd:42: Lost braces; missing escapes or markup?
    42 | {AggFunc} \code{'<func>'}: \tab\tab\tab\tab Summary function for \code{bar} type.\cr
       | ^
checkRd: (-1) cql.Rd:45: Lost braces; missing escapes or markup?
    45 | {Fit} \code{'<show_se>'}: \tab\tab\tab\tab Valid types: \code{true|false}. Fit quadratic line.\cr
       | ^
checkRd: (-1) cql.Rd:47: Lost braces; missing escapes or markup?
    47 | {ConfInt} \code{'<interval>'}: \tab\tab\tab\tab  Show error bars. Value is confidence interval value. E.g. '.95'
       | ^
Packages required but not available: 'anesrake', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) create_unit_tests.Rd:17: Lost braces; missing escapes or markup?
    17 | Create `{testthat}` test cases for the code.
       |         ^
Packages required but not available: 'config', 'yaml'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'shinytest2'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘yaml’

Package suggested but not available for checking: ‘quarto’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'roxygen2'

Packages suggested but not available for checking:
  'attachment', 'knitr', 'rmarkdown', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Lawrence Hudson <quicklizard@googlemail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Lawrence", "Hudson", "with", "contributions", "from", "Dan"),
                      family = "Reuman",
                      role = "aut"),
               person(given = "Rob",
                      family = "Emerson",
                      role = "aut"),
               person(given = "Lawrence",
                      family = "Hudson",
                      role = "cre",
                      email = "quicklizard@googlemail.com"))
as necessary.
Packages required but not available: 'spinifex', 'plotly', 'DT'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'quarto', 'knitr'

VignetteBuilder package required for checking but not installed: ‘quarto’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'ggpmisc', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'fmcsR', 'ChemmineR', 'GUniFrac'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Package suggested but not available for checking: ‘roxut’

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

Packages suggested but not available for checking:
  'ChemoSpec', 'ChemoSpec2D', 'roxut'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Haitian Xie <xht@gsm.pku.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Haitian",
                    family = "Xie",
                    role = c("aut", "cre"),
                    email = "xht@gsm.pku.edu.cn")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

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

Packages suggested but not available for checking:
  'GenomicInteractions', 'Gviz', 'countreg'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Stef van Buuren <stef.vanbuuren@tno.nl>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'ecmwfr', 'keyring'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘bruceR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Stefan Roediger <stefan.roediger@b-tu.de>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'qpcR', 'RDML', 'rmarkdown', 'spelling'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
checkRd: (-1) C316.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C317.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C60.amp.Rd:63-67: Lost braces
    63 |     40 x {
       |          ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tufte'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'optimizeR', 'oeli'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘threejs’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘factoextra’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'targets', 'DiagrammeR', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael P. Fay <mfay@niaid.nih.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Michael", "P."),
                    family = "Fay",
                    role = c("aut", "cre"),
                    email = "mfay@niaid.nih.gov")
as necessary.
Package required but not available: ‘fGarch’

Package suggested but not available for checking: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Axel Gandy <a.gandy@imperial.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Axel",
                      family = "Gandy",
                      role = c("aut", "cre"),
                      email = "a.gandy@imperial.ac.uk"),
               person(given = c("F.", "Din-Houn"),
                      family = "Lau",
                      role = "aut"))
as necessary.
Maintainer: ‘Jonathan Rosenblatt <johnros@bgu.ac.il>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jonathan",
                    family = "Rosenblatt",
                    role = c("aut", "cre"),
                    email = "johnros@bgu.ac.il")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'gt', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ari Lamstein <ari@lamsteinconsulting.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ari",
                    family = "Lamstein",
                    role = c("aut", "cre"),
                    email = "ari@lamsteinconsulting.com")
as necessary.
Maintainer: ‘Ari Lamstein <ari@lamsteinconsulting.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ari",
                    family = "Lamstein",
                    role = c("aut", "cre"),
                    email = "ari@lamsteinconsulting.com")
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Matthieu Herrmann <matthieu.herrmann@monash.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Author field differs from that derived from Authors@R
  Author:    ‘Garrick Aden-Buie [aut, cre] (<https://orcid.org/0000-0002-7111-0077>), Winston Chang [aut], Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>), Posit Software, PBC [cph, fnd] (03wc8by49)’
  Authors@R: ‘Garrick Aden-Buie [aut, cre] (ORCID: <https://orcid.org/0000-0002-7111-0077>), Winston Chang [aut], Barret Schloerke [aut] (ORCID: <https://orcid.org/0000-0001-9986-114X>), Posit Software, PBC [cph, fnd] (ROR: <https://ror.org/03wc8by49>)’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'DT', 'dygraphs', 'knitr', 'plotly', 'prettydoc', 'rmarkdown',
  'rmdformats', 'skimr'

Packages suggested but not available for checking:
  'bookdown', 'devtools', 'flexdashboard', 'pagedown', 'rolldown',
  'rticles', 'tufte', 'xaringan'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Packages suggested but not available for checking: 'spelling', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: support will be removed soon
checkRd: (-1) chunker-methods.Rd:63: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:64: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:70: Lost braces in \enumerate; meant \describe ?
Maintainer: ‘William Nickols <willnickols@college.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "William",
                    family = "Nickols",
                    role = c("aut", "cre"),
                    email = "willnickols@college.harvard.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Juris Meija <juris.meija@nrc-cnrc.gc.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Juris",
                      family = "Meija",
                      role = c("aut", "cre"),
                      email = "juris.meija@nrc-cnrc.gc.ca"),
               person(given = "Antonio",
                      family = "Possolo",
                      role = "aut"))
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘abundances2ratios.Rd’:
    http://dx.doi.org/10.1088/0026-1394/45/4/012
    https://doi.org/10.1088/1681-7575/aa634d
  File ‘at.weight.Rd’:
    http://dx.doi.org/10.1088/0026-1394/45/1/008
    https://doi.org/10.1088/1681-7575/aa634d
  File ‘ciaaw.mass.2012.Rd’:
    https://doi.org/10.1088/1674-1137/41/3/030003
  File ‘ciaaw.mass.2016.Rd’:
    https://doi.org/10.1088/1674-1137/41/3/030003
  File ‘mmm.Rd’:
    http://dx.doi.org/10.1002/sim.6789
    https://doi.org/10.1088/1681-7575/aa634d
  File ‘normalize.ratios.Rd’:
    http://dx.doi.org/10.1088/0026-1394/45/1/008
    https://doi.org/10.1088/1681-7575/aa634d
Maintainer: ‘Gabriele Lubatti <gabriele.lubatti@helmholtz-muenchen.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gabriele",
                    family = "Lubatti",
                    role = c("aut", "cre"),
                    email = "gabriele.lubatti@helmholtz-muenchen.de")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'plotly', 'Seurat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jeffrey Durieux <durieux.jeffrey@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jeffrey",
                      family = "Durieux",
                      role = c("aut", "cre"),
                      email = "durieux.jeffrey@gmail.com"),
               person(given = "Tom",
                      family = "Wilderjans",
                      role = "aut"),
               person(given = c("Juan", "Claramunt"),
                      family = "Gonzalez",
                      role = "ctb"))
as necessary.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Stefan Konigorski <stefan.konigorski@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Dadong Zhang <dzhang4@illumina.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dadong",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "dzhang4@illumina.com"),
               person(given = "Jingye",
                      family = "Wang",
                      role = "aut",
                      email = "jwang16@illumina.com"),
               person(given = "Suqin",
                      family = "Cai",
                      role = "aut",
                      email = "scai1@illumina.com"),
               person(given = "Johan",
                      family = "Surtihadi",
                      role = "aut",
                      email = "jsurtihadi@illumina.com"))
as necessary.
Package required but not available: ‘kableExtra’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'modelsummary', 'gtsummary', 'knitr', 'rmarkdown', 'pkgdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Found the following significant warnings:
  calculateAJ_Rcpp.cpp:520:60: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ reading between 8 and 34359738368 bytes from a region of size 0 [-Wstringop-overread]
  calculateAJ_Rcpp.cpp:515:60: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ reading between 8 and 34359738368 bytes from a region of size 0 [-Wstringop-overread]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cifmodeling.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-15 (Debian 15.2.0-9) 15.2.0’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) ec.datalag.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{prepares Dy y_1 Dy_1 ... Dy_{nlag-1} for estimation}
       |                                    ^
checkRd: (-1) ec.datalag.Rd:15: Lost braces
    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                      ^
checkRd: (-1) ec.datalag.Rd:15: Lost braces; missing escapes or markup?
    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                                          ^
checkRd: (-1) lagn.Rd:21: Lost braces; missing escapes or markup?
    21 |              REM: alternative to "lead-lag" {dplyr} which applies to vector y
       |                                             ^
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'rgl'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

Packages suggested but not available for checking:
  'covr', 'htmlwidgets', 'manipulateWidget', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'devtools', 'ggExtra'

Packages suggested but not available for checking:
  'knitr', 'minfi', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘long_est.R’
Packages required but not available: 'tmle', 'SuperLearner'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Vishal H. Oza <vishoza@uab.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Vishal", "H."),
                      family = "Oza",
                      role = c("aut", "cre"),
                      email = "vishoza@uab.edu"),
               person(given = "Roshan",
                      family = "Darji",
                      role = "aut"),
               person(given = c("Brittany", "N."),
                      family = "Lasseigne",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'FactoMineR', 'factoextra'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘CIPerm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dset
> ### Title: Permutation-methods summary statistics
> ### Aliases: dset
> 
> ### ** Examples
> 
> x <- c(19, 22, 25, 26)
> y <- c(23, 33, 40)
> demo <- dset(x, y, returnData = TRUE)
> knitr::kable(demo, digits = 2)
Error in loadNamespace(x) : there is no package called ‘knitr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Toshiaki Ara <toshiaki.ara@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Toshiaki",
                    family = "Ara",
                    role = c("aut", "cre"),
                    email = "toshiaki.ara@gmail.com")
as necessary.
checkRd: (-1) CIplot.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.
       |                       ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rJava’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘functions.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'usethis', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Robert Fitak <rfitak9@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Maria Mercedes Gregorio-Dominguez <mercedes@itam.mx>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Juan", "Jose"),
                      family = "Fernandez-Duran",
                      role = "aut"),
               person(given = c("Maria", "Mercedes"),
                      family = "Gregorio-Dominguez",
                      role = c("aut", "cre"),
                      email = "mercedes@itam.mx"))
as necessary.
Maintainer: ‘Azade Ghazanfarihesari <azade_ghazanfari@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Azade",
                      family = "Ghazanfarihesari",
                      role = c("aut", "cre"),
                      email = "azade_ghazanfari@yahoo.com"),
               person(given = c("Majid", "Sarmad-", "Ferdowsi", "University", "Of"),
                      family = "Mashhad",
                      role = "aut"))
as necessary.
Maintainer: ‘Mario Santoro <santoro.ma@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/santoroma/CircSpaceTime
which should likely be
  https://github.com/santoroma/CircSpaceTime/issues
instead.
Specified C++11: support will be removed soon
Maintainer: ‘Evandro Konzen <circularev.r@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Evandro",
                    family = "Konzen",
                    role = c("aut", "cre"),
                    email = "circularev.r@gmail.com")
as necessary.
Package required but not available: ‘NPCirc’

Packages suggested but not available for checking:
  'plotly', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlTable’

Packages suggested but not available for checking:
  'covr', 'kableExtra', 'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘cisp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ssh_marginalcontri
> ### Title: spatial association marginal contributions derived from spatial
> ###   stratified heterogeneity
> ### Aliases: ssh_marginalcontri
> 
> ### ** Examples
> 
> NTDs1 = sf::st_as_sf(gdverse::NTDs, coords = c('X','Y'))
> g = ssh_marginalcontri(incidence ~ ., data = NTDs1, cores = 1)
> g
***   SSH Marginal Contributions    Error in loadNamespace(x) : there is no package called ‘knitr’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Neal Haddaway <nealhaddaway@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'MESS', 'networkD3'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘test-all.R’ [1s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("citecorp")
  Loading required package: citecorp
  Error in `source_dir()`:
  ! Failed to evaluate './helper-citecorp.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("citecorp")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at ./helper-citecorp.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<S3: packageNotFoundError>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'rmarkdown', 'knitr'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'rmarkdown', 'plotly', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2', 'yaml'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [9s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(civis)
  > 
  > test_check("civis")
  Saving _problems/test_reports-90.R
  Saving _problems/test_reports-99.R
  [ FAIL 2 | WARN 6 | SKIP 0 | PASS 1057 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_reports.R:90:5'): parse_front_matter parses yaml correctly ───
  Expected `parse_front_matter(textConnection(rmd_a))` to equal `expect_a`.
  Differences:
  names for current but not for target
  Length mismatch: comparison on first 0 components
  ── Failure ('test_reports.R:99:5'): parse_front_matter handles parsing errors with warning ──
  `parse_front_matter(textConnection(rmd_a))` produced unexpected warnings.
  Expected match: Failed to parse Civis metadata from Rmarkdown file: Scanner error: mapping values are not allowed in this context at line 2, column 11
  Actual values:
  * Failed to parse Civis metadata from Rmarkdown file: there is no package called 'yaml'
  
  [ FAIL 2 | WARN 6 | SKIP 0 | PASS 1057 ]
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Thomas Wiemann <wiemann@uchicago.edu>’

The Description field contains
  proposed by Wiemann (2023) <arXiv:2311.17021>. CIV allows for optimal
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Stefan Konigorski <stefan.konigorski@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘randomForestSRC’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Raphiel Murden <rmurden@emory.edu>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Anton Strezhnev <astrezhnev@uchicago.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Soubhik",
                      family = "Barari",
                      role = "aut"),
               person(given = "Elissa",
                      family = "Berwick",
                      role = "aut"),
               person(given = "Jens",
                      family = "Hainmueller",
                      role = "aut"),
               person(given = "Daniel",
                      family = "Hopkins",
                      role = "aut"),
               person(given = "Sean",
                      family = "Liu",
                      role = "aut"),
               person(given = "Anton",
                      family = "Strezhnev",
                      role = c("aut", "cre"),
                      email = "astrezhnev@uchicago.edu"),
               person(given = "Teppei",
                      family = "Yamamoto",
                      role = "aut"))
as necessary.
Package required but not available: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Hong Zhang <hzhang@wpi.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hong",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "hzhang@wpi.edu"),
               person(given = "Judong",
                      family = "Shen",
                      role = "aut"))
as necessary.
Maintainer: ‘Haoyu Zhang <andrew.haoyu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ni",
                      family = "Zhao",
                      role = "aut"),
               person(given = "Haoyu",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "andrew.haoyu@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jonathan M. Lees<jonathan.lees@unc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Jonathan", "M."),
                    family = "Lees",
                    role = c("aut", "cre"),
                    email = "jonathan.lees@unc.edu")
as necessary.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘compute_cluster_composition.R’ ‘extract_ids_vector.R’
    ‘perform_clustering.R’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running examples in ‘CLA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: muSigmaGarch
> ### Title: Compute (mu, Sigma) for a Set of Assets via GARCH fit
> ### Aliases: muSigmaGarch
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> if(requireNamespace("FRAPO")) {
+   data(NASDAQ, package = "FRAPO")
+   ## 12 randomly picked stocks from NASDAQ data
+   iS <- if(FALSE) {  ## created (w/ warning, in new R)  by
+     RNGversion("3.5.0"); set.seed(17); iS <- sample(ncol(NASDAQ), 12)
+   } else c(341L, 2126L, 1028L, 1704L, 895L, 1181L, 454L, 410L, 1707L, 425L, 950L, 5L)
+   X. <- NASDAQ[, iS]
+   muSig <- muSigmaGarch(X.)
+   stopifnot(identical(names(muSig$mu), names(NASDAQ)[iS]),
+             identical(dim(muSig$covar), c(12L,12L)),
+      all.equal(unname(muSig$mu),
+                c(  7.97, -4.05, -14,     21.5, -5.36, -15.3,
+                  -15.9,  11.8,   -1.64, -14,    3.13, 121) / 10000,
+                tol = 0.0015))
+ }
Loading required namespace: FRAPO
Loading required namespace: fGarch
Failed with error:  ‘there is no package called ‘fGarch’’
Error in muSigmaGarch(X.) : 
  muSigmaGarch() needs the 'fGarch' package installed
Execution halted
Maintainer: ‘Gaurav Sood <gsood07@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) get_langs.Rd:13: Lost braces
    13 | character vector listing all the languages that tag API call supports. See \code{\link{tag_images}} and code{\link{tag_image_urls}}
       |                                                                                                             ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rms'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'gt', 'reactable', 'reactablefmtr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

Depends: includes the non-default packages:
  'C50', 'car', 'caret', 'corrplot', 'doParallel', 'dplyr', 'e1071',
  'ggplot2', 'gt', 'ipred', 'MachineShop', 'magrittr', 'parallel',
  'pls', 'purrr', 'randomForest', 'ranger', 'reactable',
  'reactablefmtr', 'scales', 'tidyr', 'tree'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Brian Ripley <Brian.Ripley@R-project.org>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Chris J. Lloyd <c.lloyd@mbs.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Chris", "J."),
                    family = "Lloyd",
                    role = c("aut", "cre"),
                    email = "c.lloyd@mbs.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘as_raster.Rd’ ‘clc.R’ ‘clc_category.R’ ‘clc_raster.R’ ‘copy_to.Rd’
    ‘cut_to_extent.Rd’ ‘get_colors.Rd’ ‘get_levels.Rd’ ‘get_raster.Rd’
    ‘plot_clc.Rd’ ‘prepare_plot.Rd’ ‘save_to.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Florencia I. Pozzi <florenciapoz@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Florencia", "I."),
                      family = "Pozzi",
                      role = c("aut", "cre"),
                      email = "florenciapoz@hotmail.com"),
               person(given = c("Silvina", "A."),
                      family = "Felitti",
                      role = "aut"))
as necessary.
Maintainer: ‘Sherry Zhao <sxzhao@gwu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sherry",
                    family = "Zhao",
                    role = c("aut", "cre"),
                    email = "sxzhao@gwu.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'htmlwidgets', 'kableExtra', 'knitr', 'lintr', 'reactable',
  'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘cleanepi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_date_sequence
> ### Title: Checks whether the order in a sequence of date events is
> ###   chronological. order.
> ### Aliases: check_date_sequence
> 
> ### ** Examples
> 
> # import the data
> data <- readRDS(system.file("extdata", "test_df.RDS", package = "cleanepi"))
> 
> # standardize the date values
> data <- data %>%
+   standardize_dates(
+     target_columns  = c("date_first_pcr_positive_test", "date.of.admission"),
+     error_tolerance = 0.4,
+     format = NULL,
+     timeframe = NULL
+   )
! Detected 4 values that comply with multiple formats and no values that are
  outside of the specified time frame.
ℹ Enter `print_report(data = dat, "date_standardization")` to access them,
  where "dat" is the object used to store the output from this operation.
> 
> # check whether all admission dates come after the test dates
> good_date_sequence <- check_date_sequence(
+   data = data,
+   target_columns = c("date_first_pcr_positive_test", "date.of.admission")
+ )
! Detected 2 incorrect date sequences at lines: "6, 8".
ℹ Enter `print_report(data = dat, "incorrect_date_sequence")` to access them,
  where "dat" is the object used to store the output from this operation.
> 
> # display rows where admission dates do not come after the test dates
> print_report(
+   data = good_date_sequence,
+   what = "incorrect_date_sequence"
+ )
Error in `print_report()`:
✖ The reactable package is required for printing the report.
Backtrace:
    ▆
 1. └─cleanepi::print_report(data = good_date_sequence, what = "incorrect_date_sequence")
 2.   └─cli::cli_abort(c(x = tr_("The {.pkg reactable} package is required for printing the report.")))
 3.     └─rlang::abort(...)
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Taylor B. Arnold <tarnold2@richmond.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Taylor", "B."),
                    family = "Arnold",
                    role = c("aut", "cre"),
                    email = "tarnold2@richmond.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘cleaner’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'rasciidoc', 'rmarkdown', 'usethis'

VignetteBuilder package required for checking but not installed: ‘rasciidoc’
Running examples in ‘cleanr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_package
> ### Title: Check a Package
> ### Aliases: check_package
> 
> ### ** Examples
> 
> # create a fake package first:
> package_path <- file.path(tempdir(), "fake")
> usethis::create_package(package_path, fields = NULL,
+                         rstudio = FALSE, open = FALSE)
Error in loadNamespace(x) : there is no package called ‘usethis’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael P.B. Gallaugher <gallaump@mcmaster.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Michael", "P.B."),
                      family = "Gallaugher",
                      role = c("aut", "cre"),
                      email = "gallaump@mcmaster.ca"),
               person(given = c("Paul", "D."),
                      family = "McNicholas",
                      role = "aut"))
as necessary.

The Description field contains
  <arXiv:1802.04849>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘fBasics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Hannah Owens <hannah.owens@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Xi (Rossi) Luo <xi.rossi.luo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("T.", "Tony"),
                      family = "Cai",
                      role = "aut"),
               person(given = "Weidong",
                      family = "Liu",
                      role = "aut"),
               person(given = "Xi",
                      family = "Luo",
                      role = "aut",
                      comment = "Rossi"),
               person(given = "Xi",
                      family = "Luo",
                      role = "cre",
                      email = "xi.rossi.luo@gmail.com",
                      comment = "Rossi"))
as necessary.
Maintainer: ‘Fergus Reig-Gracia <fergusrg@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Fergus",
                      family = "Reig-Gracia",
                      role = c("aut", "cre"),
                      email = "fergusrg@gmail.com"),
               person(given = c("Sergio", "M."),
                      family = "Vicente-Serrano",
                      role = "aut"),
               person(given = "Fernando",
                      family = "Dominguez-Castro",
                      role = "aut"),
               person(given = "Joaquin",
                      family = "Bedia-Jiménez",
                      role = "ctb"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘lares’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'bookdown', 'clinUtils', 'htmlwidgets', 'knitr', 'plotly',
  'rmarkdown', 'yaml'

Packages suggested but not available for checking:
  'inTextSummaryTable', 'patientProfilesVis', 'DT'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Daewoo Pak <heavyrain.pak@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Daewoo",
                      family = "Pak",
                      role = c("aut", "cre"),
                      email = "heavyrain.pak@gmail.com"),
               person(given = "Song",
                      family = "Yang",
                      role = "aut"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘ClinicalTrialSummary-package.Rd’:
    \keyword{Survival analysis, Clinical trials, Hazar [TRUNCATED]
Maintainer: ‘Anu Mishra <anmishra@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Anu",
                    family = "Mishra",
                    role = c("aut", "cre"),
                    email = "anmishra@uw.edu")
as necessary.
Packages required but not available: 'flextable', 'knitr'

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mike Malek-Ahmadi <michael.malekahmadi@bannerhealth.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mike",
                      family = "Malek-Ahmadi",
                      role = c("aut", "cre"),
                      email = "michael.malekahmadi@bannerhealth.com"),
               person(given = "Kjera",
                      family = "Schack",
                      role = "aut",
                      email = "kgschack@asu.edu"))
as necessary.
Maintainer: ‘Jim Lemon <drjimlemon@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jim",
                      family = "Lemon,",
                      role = "aut",
                      email = "drjimlemon@gmail.com"),
               person(given = "Jim",
                      family = "Lemon",
                      role = "cre",
                      email = "drjimlemon@gmail.com"))
as necessary.
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                   ^
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                                 ^
Maintainer: ‘Karandeep Singh <kdpsingh@umich.edu>’

The Description field contains
  embeddings developed by Beam (2018) <arXiv:1804.01486>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘rmarkdown’

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'plotly', 'rmarkdown', 'flextable'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jens Lange <lange.jens@outlook.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'qgraph', 'lessR'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Casey M. Jelsema <jelsema.casey@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rlist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Haolun Shi <shl2003@connect.hku.hk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Haolun",
                      family = "Shi",
                      role = c("aut", "cre"),
                      email = "shl2003@connect.hku.hk"),
               person(given = "Guosheng",
                      family = "Yin",
                      role = "aut"))
as necessary.
Maintainer: ‘Stephen Reid <sreid1652@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Stephen",
                      family = "Reid",
                      role = c("aut", "cre"),
                      email = "sreid1652@gmail.com"),
               person(given = "Robert",
                      family = "Tibshirani",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) print.clogitL1.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.clogitL1.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.clogitL1.Rd:23: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
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  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cloud_drive_download_bulk.Rd’ ‘cloud_drive_read_bulk.Rd’
    ‘cloud_drive_upload_bulk.Rd’ ‘cloud_drive_write_bulk.Rd’
    ‘cloud_s3_download_bulk.Rd’ ‘cloud_s3_read_bulk.Rd’
    ‘cloud_s3_upload_bulk.Rd’ ‘cloud_s3_write_bulk.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'tfruns', 'config', 'yaml'

Packages suggested but not available for checking:
  'tensorflow', 'keras', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cb_participant_count.Rd:13: Lost braces
    13 | \item{query}{A phenotype query defined using the code{\link{phenotype}} function and logic operators (see example below)}
       |                                                      ^
checkRd: (-1) phenotype.Rd:10: Lost braces
    10 | \item{id}{A single phenotype id. Possible phenotyoes can be explored using the code{\link{cb_search_phenotypes}} function}
       |                                                                                    ^
Package required but not available: ‘keyring’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Christian Panse <cp@fgcz.ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Christian",
                      family = "Panse",
                      role = c("aut", "cre"),
                      email = "cp@fgcz.ethz.ch"),
               person(given = "Ermir",
                      family = "Qeli",
                      role = "aut",
                      email = "ermir.qeli@gmail.com"))
as necessary.
Maintainer: ‘Amandine Pierrot <amandine.m.pierrot@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Amandine", "Pierrot", "with", "contributions", "and/or", "help", "from", "Qiwei"),
                      family = "Yao",
                      role = "aut"),
               person(given = "Haeran",
                      family = "Cho",
                      role = "aut"),
               person(given = "Yannig",
                      family = "Goude",
                      role = "aut"),
               person(given = "Tony",
                      family = "Aldon.",
                      role = "aut"),
               person(given = "Amandine",
                      family = "Pierrot",
                      role = "cre",
                      email = "amandine.m.pierrot@gmail.com"))
as necessary.
checkRd: (-1) clr.Rd:24: Lost braces
    24 | the sense that its Karhunen-Lo\`{e}ve decomposition has qx terms only.}
       |                                 ^
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bias_df_combined.R’ ‘create_table_ep_15.R’
    ‘precision_calculate_aov_info.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Simiao Ye <simiao.ye@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Simiao",
                      family = "Ye",
                      role = c("aut", "cre"),
                      email = "simiao.ye@gmail.com"),
               person(given = "Jingning",
                      family = "Mei",
                      role = "aut"))
as necessary.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
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  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Pengyi Yang <yangpy7@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Pengyi",
                    family = "Yang",
                    role = c("aut", "cre"),
                    email = "yangpy7@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'lintr', 'prettydoc', 'rgl', 'rmarkdown',
  'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jan Fojtik <9afojtik@gmail.com>’

The Description field contains
  Sobisek, Stachova, Fojtik (2018) <arXiv:1807.05926>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Emmanuel S Tsyawo <estsyawo@temple.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Emmanuel", "S"),
                      family = "Tsyawo",
                      role = c("aut", "cre"),
                      email = "estsyawo@temple.edu"),
               person(given = "Abdul-Nasah",
                      family = "Soale",
                      role = "aut"))
as necessary.
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Matthieu Marbac <matthieu.marbac-lourdelle@ensai.fr>’

The Description field contains
  Marbac et al. (2020) <arXiv:2012.14159> are implemented.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Martí Renedo Mirambell <marti.renedo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Martí", "Renedo"),
                    family = "Mirambell",
                    role = c("aut", "cre"),
                    email = "marti.renedo@gmail.com")
as necessary.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'DT', 'gprofiler2', 'plotly', 'Seurat'

Packages suggested but not available for checking:
  'colourpicker', 'devtools', 'monocle3', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘survminer’

Packages suggested but not available for checking:
  'covr', 'knitr', 'plotly', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Frederick Novomestky <fnovomes@poly.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Frederick",
                    family = "Novomestky",
                    role = c("aut", "cre"),
                    email = "fnovomes@poly.edu")
as necessary.
Maintainer: ‘Weiliang Qiu <weiliang.qiu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Weiliang",
                      family = "Qiu",
                      role = c("aut", "cre"),
                      email = "weiliang.qiu@gmail.com"),
               person(given = "Harry",
                      family = "Joe.",
                      role = "aut",
                      email = "harry@stat.ubc.ca"))
as necessary.
Package required but not available: ‘factoextra’

Packages suggested but not available for checking:
  'clusterProfiler', 'knitr', 'rmarkdown', 'Seurat', 'WGCNA'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gaston Quero <gastonquero@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gaston",
                      family = "Quero",
                      role = c("aut", "cre"),
                      email = "gastonquero@gmail.com"),
               person(given = "Sebastian",
                      family = "Simondi",
                      role = "aut",
                      email = "sebastian.simondi@gmail.com"),
               person(given = c("with", "contributions", "from", "Victoria"),
                      family = "Bonnecarrere",
                      role = "aut"),
               person(given = "Lucia",
                      family = "Gutierrez",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Found the following files/directories:
  ‘clusterhap_reports’
Maintainer: ‘Jakob Raymaekers <j.raymaekers@maastrichtuniversity.nl>’

The Description field contains
  <arXiv:2010.00950>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Specified C++11: support will be removed soon
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |      ^
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |                ^
checkRd: (-1) HTKmeans.Rd:63: Lost braces
    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |      ^
checkRd: (-1) HTKmeans.Rd:63: Lost braces
    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |                ^
checkRd: (-1) HTKmeans.Rd:64: Lost braces
    64 | \item{itnb }{The number of iterations executed until convergence}
       |      ^
checkRd: (-1) HTKmeans.Rd:64: Lost braces
    64 | \item{itnb }{The number of iterations executed until convergence}
       |             ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |      ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |                  ^
Maintainer: ‘Luis Alfonso Perez Martos <lapm0001@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Luis", "Alfonso", "Perez"),
                    family = "Martos",
                    role = c("aut", "cre"),
                    email = "lapm0001@gmail.com",
                    comment = c(ORCID = "0000-0002-5154-6105"))
as necessary.
Package required but not available: ‘FactoMineR’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'missMDA', 'bookdown'

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Evelina Gabasova <egabasova@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Evelina",
                    family = "Gabasova",
                    role = c("aut", "cre"),
                    email = "egabasova@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Sandipan Dutta <sandipan.dutta07@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sandipan",
                      family = "Dutta",
                      role = c("aut", "cre"),
                      email = "sandipan.dutta07@gmail.com"),
               person(given = "Somnath",
                      family = "Datta",
                      role = "aut"))
as necessary.
Maintainer: ‘Rob Tibshirani <tibs@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Amy",
                      family = "Kapp",
                      role = "aut",
                      email = "Amy_Kapp@hotmail.com"),
               person(given = "Rob",
                      family = "Tibshirani",
                      role = c("aut", "cre"),
                      email = "tibs@stanford.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Justin Esarey <justin@justinesarey.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Etienne Lord <m.etienne.lord@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Etienne",
                      family = "Lord",
                      role = c("aut", "cre"),
                      email = "m.etienne.lord@gmail.com"),
               person(given = "Matthieu",
                      family = "Willems",
                      role = "aut"),
               person(given = "Francois-Joseph",
                      family = "Lapointe",
                      role = "aut"),
               person(given = "Vladimir",
                      family = "Makarenkov",
                      role = "aut"))
as necessary.
Packages required but not available: 'factoextra', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Oliver Pfaffel <opfaffel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Oliver",
                    family = "Pfaffel",
                    role = c("aut", "cre"),
                    email = "opfaffel@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘knitr’

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  'ggExtra', 'rmarkdown', 'Hmisc', 'spelling', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
Maintainer: ‘Gero Szepannek <gero.szepannek@web.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gero",
                      family = "Szepannek",
                      role = c("aut", "cre"),
                      email = "gero.szepannek@web.de"),
               person(given = "Rabea",
                      family = "Aschenbruck",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Muhammad Atif <muhammad96_atif@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Muhammad",
                    family = "Atif",
                    role = c("aut", "cre"),
                    email = "muhammad96_atif@yahoo.com")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Angelos Markos <amarkos@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Angelos",
                      family = "Markos",
                      role = c("aut", "cre"),
                      email = "amarkos@gmail.com"),
               person(given = c("Alfonso", "Iodice"),
                      family = "D'Enza",
                      role = "aut"),
               person(given = "Michel",
                      family = "van de Velden",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Seurat', 'covr', 'pkgdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Dan S. Reznik <dreznik@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Dan", "S."),
                    family = "Reznik",
                    role = c("aut", "cre"),
                    email = "dreznik@gmail.com")
as necessary.
Maintainer: ‘Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kartikeya",
                    family = "Bolar",
                    role = c("aut", "cre"),
                    email = "kartikeya.bolar@tapmi.edu.in")
as necessary.
Package required but not available: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'bookdown', 'covr', 'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Evelyne Vigneau <evelyne.vigneau@oniris-nantes.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Evelyne",
                      family = "Vigneau",
                      role = c("aut", "cre"),
                      email = "evelyne.vigneau@oniris-nantes.fr"),
               person(given = "Mingkun",
                      family = "Chen",
                      role = "ctb"),
               person(given = "Veronique",
                      family = "Cariou",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Vasyl Pihur <vpihur@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Guy",
                      family = "Brock",
                      role = "aut",
                      email = "guy.brock@louisville.edu"),
               person(given = "Vasyl",
                      family = "Pihur",
                      role = c("aut", "cre"),
                      email = "vpihur@gmail.com"),
               person(given = "Susmita",
                      family = "Datta",
                      role = "aut",
                      email = "susmita.datta@louisville.edu"),
               person(given = "Somnath",
                      family = "Datta",
                      role = "aut",
                      email = "somnath.datta@louisville.edu"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/clv.Rcheck/00install.out’ for details.
Cannot process vignettes
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  'covr', 'knitr', 'rmarkdown'

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Maintainer: ‘Olaf Mersmann <olafm@statistik.tu-dortmund.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Heike",
                      family = "Trautmann",
                      role = "aut",
                      email = "trautmann@statistik.tu-dortmund.de"),
               person(given = "Olaf",
                      family = "Mersmann",
                      role = c("aut", "cre"),
                      email = "olafm@statistik.tu-dortmund.de"),
               person(given = "David",
                      family = "Arnu",
                      role = "aut",
                      email = "david.arnu@statistik.tu-dortmund.de"))
as necessary.
Package required but not available: ‘factoextra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) CMAPSS.Rd:10: Lost braces
    10 | \item \code{train}{ a list of class "hhsmm.data" as the train dataset}
       |                   ^
checkRd: (-1) CMAPSS.Rd:11: Lost braces
    11 | \item \code{test}{ a list of class "hhsmm.data" as the test dataset}
       |                  ^
checkRd: (-1) CMAPSS.Rd:12: Lost braces
    12 | \item \code{subsets}{ a matrix containig the number of units in each subset of the CMAPSS data set (FD001-FD004) for the train and test datasets}
       |                     ^
Maintainer: ‘Raphaël Bonnet <raphael.bonnet@univ-cotedazur.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Raphaël",
                      family = "Bonnet",
                      role = c("aut", "cre"),
                      email = "raphael.bonnet@univ-cotedazur.fr"),
               person(given = "Jean-François",
                      family = "Peyron",
                      role = c("aut", "ths")))
as necessary.
Cannot process vignettes
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
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checkRd: (-1) cmb.search.Rd:50: Lost braces; missing escapes or markup?
    50 |   \item{order}{applied conditioning order {length p}}
       |                                           ^
'library' or 'require' calls not declared from:
  ‘HDclassif’ ‘MixSim’ ‘mclust’
Maintainer: ‘Matthew T. Pratola <mpratola@stat.osu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Matthew", "T."),
                    family = "Pratola",
                    role = c("aut", "cre", "cph"),
                    email = "mpratola@stat.osu.edu")
as necessary.
checkRd: (-1) gp.realize.Rd:20: Lost braces; missing escapes or markup?
    20 | The list \code{l.v} is created by \code{makedistlist()} from a {n x p} design matrix on which to generate the unconditional GP realization.  The correlation parameters take on values in \code{(0,1)} and use the Gaussian correlation model, calculated as \code{rho^d(xi,xj)^2}.  This helper function is used to create the demonstration data used in the example for \code{calibrate()}.
       |                                                                ^
Maintainer: ‘Spencer Nystrom <nystromdev@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/snystrom/cmdfun
which should likely be
  https://github.com/snystrom/cmdfun/issues
instead.
Package required but not available: ‘usethis’

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Maintainer: ‘Simon Mak <sm769@duke.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Simon",
                    family = "Mak",
                    role = c("aut", "cre"),
                    email = "sm769@duke.edu")
as necessary.
Specified C++11: support will be removed soon
Maintainer: ‘Felix Held <felix.held@gmail.com>’

The Description field contains
  al. (2014) <arXiv:1312.5921>.  The package can also be used to learn
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘David Cortes <david.cortes.rivera@gmail.com>’

The Description field contains
  extensions of the original model (Cortes, (2018) <arXiv:1809.00366>)
  'implicit features' (Rendle, Zhang, Koren, (2019) <arXiv:1905.01395>),
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Anh Tuan Bui <atbui@u.northwestern.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Anh", "Tuan"),
                    family = "Bui",
                    role = c("aut", "cre"),
                    email = "atbui@u.northwestern.edu")
as necessary.

The Description field contains
  (2021) <arXiv:2111.13646> or closed-form solution in Bui (2022)
  (2021) <arXiv:2111.13646>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) bvp.Rd:24: Lost braces
    24 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivp.Rd:38: Lost braces
    38 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivpsys.Rd:29: Lost braces
    29 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
Cannot process vignettes
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VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘LiLin-Yin <ylilin@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(family = "LiLin-Yin",
                    role = c("aut", "cre"),
                    email = "ylilin@163.com")
as necessary.
Maintainer: ‘Yiran Zhang <yiz038@health.ucsd.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yiran",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "yiz038@health.ucsd.edu"),
               person(given = "Ronghui",
                      family = "Xu",
                      role = "aut"))
as necessary.
Cannot process vignettes
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Please add one, modifying
  Authors@R: c(person(given = "Stephan",
                      family = "Dlugosz",
                      role = c("aut", "cre"),
                      email = "stephan.dlugosz@googlemail.com"),
               person(given = "Limin",
                      family = "Peng",
                      role = "aut"),
               person(given = "Ruosha",
                      family = "Li",
                      role = "aut"),
               person(given = "Shuolin",
                      family = "Shi",
                      role = "ctb"))
as necessary.
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
Maintainer: ‘Bob Gray <gray@jimmy.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bob",
                    family = "Gray",
                    role = c("aut", "cre"),
                    email = "gray@jimmy.harvard.edu")
as necessary.
Maintainer: ‘Wangqian Ju <wju@iastate.edu>’

Package CITATION file contains call(s) to old-style citEntry().  Please
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VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘cmpsR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute_diff_phase
> ### Title: Compute a Statistic for the Foreground Phase and the Background
> ###   Phases
> ### Aliases: compute_diff_phase
> 
> ### ** Examples
> 
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Andrey Paramonov <paramon@acdlabs.ru>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andrey",
                    family = "Paramonov",
                    role = c("aut", "cre"),
                    email = "paramon@acdlabs.ru")
as necessary.
Maintainer: ‘Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kartikeya",
                    family = "Bolar",
                    role = c("aut", "cre"),
                    email = "kartikeya.bolar@tapmi.edu.in")
as necessary.
Package required but not available: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Cannot process vignettes
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  'knitr', 'lintr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘basis.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
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Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Mohsin Vindhani <mohsin@utiligize.com>’

Package CITATION file contains call(s) to old-style personList() or
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Package CITATION file contains call(s) to old-style citEntry().  Please
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VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Xiaotian Zhu <xiaotian.zhu.psualum@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Xiaotian",
                    family = "Zhu",
                    role = c("aut", "cre"),
                    email = "xiaotian.zhu.psualum@gmail.com")
as necessary.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Ana Belen Nieto Librero <ananieto@usal.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ana", "Belen", "Nieto"),
                      family = "Librero",
                      role = c("aut", "cre"),
                      email = "ananieto@usal.es"),
               person(given = "Priscila",
                      family = "Willems",
                      role = "aut",
                      email = "pwillems@bariloche.inta.gov.ar"),
               person(given = c("Purificacion", "Galindo"),
                      family = "Villardon",
                      role = "aut",
                      email = "pgalindo@usal.es"))
as necessary.
Packages required but not available: 'rgl', 'shapes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cnlt.reg.Rd:43: Lost braces
    43 | \emph{Technometrics}, bold{60} (1), 48-60, DOI 10.1080/00401706.2017.1281846.\cr\cr
       |                           ^
checkRd: (-1) fwtnppermC.Rd:35: Lost braces
    35 | Given \eqn{n} points on a line, \env{x}, each with a corresponding env{f} value this function computes
       |                                                                       ^
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Guoli Sun <guolisun87@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alex",
                      family = "Krasnitz",
                      role = "aut"),
               person(given = "Guoli",
                      family = "Sun",
                      role = c("aut", "cre"),
                      email = "guolisun87@gmail.com"))
as necessary.
Maintainer: ‘JiaSheng Zhang <zhangjiasheng0509@outlook.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "JiaSheng",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "zhangjiasheng0509@outlook.com",
                      comment = "<zhangjiasheng0509@outlook.com>"),
               person(given = "SiWei",
                      family = "Deng",
                      role = "aut"),
               person(given = "Feng",
                      family = "Yu",
                      role = "aut"),
               person(given = "YangYang",
                      family = "Zhang",
                      role = "aut"))
as necessary.
Cannot process vignettes
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘James Dalgleish <james.dalgleish@nih.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "James",
                      family = "Dalgeish",
                      role = "aut"),
               person(given = "Yonghong",
                      family = "Wang",
                      role = "aut"),
               person(given = "Jack",
                      family = "Zhu",
                      role = "aut"),
               person(given = "Paul",
                      family = "Meltzer",
                      role = "aut"),
               person(given = "James",
                      family = "Dalgleish",
                      role = "cre",
                      email = "james.dalgleish@nih.gov"))
as necessary.
Packages required but not available:
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  'knitr', 'rmarkdown', 'HiCseg', 'visNetwork', 'plotly',
  'GenomicFeatures', 'DT', 'heatmaply', 'htmlwidgets',
  'BSgenome.Hsapiens.UCSC.hg19'

VignetteBuilder package required for checking but not installed: ‘knitr’

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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Emmanuel Paradis <Emmanuel.Paradis@ird.fr>’

Package CITATION file contains call(s) to old-style personList() or
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Package CITATION file contains call(s) to old-style citEntry().  Please
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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VignetteBuilder package required for checking but not installed: ‘knitr’
Unknown package ‘designmatch’ in Rd xrefs
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Maintainer: ‘Alessandra Cabassi <alessandra.cabassi@mrc-bsu.cam.ac.uk>’

Package CITATION file contains call(s) to old-style personList() or
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Package CITATION file contains call(s) to old-style citEntry().  Please
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Package required but not available: ‘DT’

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

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
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Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Birk Diedenhofen <mail@birkdiedenhofen.de>’

The Description field contains
  http://comparingcronbachalphas.org. A plugin for the R GUI and IDE
  RKWard is included. Please install RKWard from https:// rkward.kde.org
Please enclose URLs in angle brackets (<...>).
Package required but not available: ‘survminer’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
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Maintainer: ‘Elliott Gordon-Rodriguez <eg2912@columbia.edu>’

Package CITATION file contains call(s) to old-style personList() or
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Package CITATION file contains call(s) to old-style citEntry().  Please
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VignetteBuilder package required for checking but not installed: ‘knitr’
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VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) educFM.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:23: Lost braces in \itemize; meant \describe ?
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Maintainer: ‘Martyn Plummer <martyn.plummer@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
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Package CITATION file contains call(s) to old-style citEntry().  Please
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Package required but not available: ‘knitr’

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Maintainer: ‘Lars Ronnegard <lrn@du.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Lars",
                    family = "Ronnegard",
                    role = c("aut", "cre"),
                    email = "lrn@du.se")
as necessary.
Package required but not available: ‘flextable’

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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gabriel Becker <gabembecker@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Duncan", "Temple"),
                      family = "Lang",
                      role = "aut"),
               person(given = "Roger",
                      family = "Peng",
                      role = "aut"),
               person(given = "Deborah",
                      family = "Nolan",
                      role = "aut"),
               person(given = "Gabriel",
                      family = "Becker",
                      role = c("aut", "cre"),
                      email = "gabembecker@gmail.com"))
as necessary.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'visOmopResults', 'knitr', 'rmarkdown', 'spelling', 'gt',
  'flextable'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'details', 'knitr', 'printr', 'rmarkdown', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Daniel Kaschek <daniel.kaschek@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Daniel",
                    family = "Kaschek",
                    role = c("aut", "cre"),
                    email = "daniel.kaschek@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Luke Tierney <luke-tierney@uiowa.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Luke",
                    family = "Tierney",
                    role = c("aut", "cre"),
                    email = "luke-tierney@uiowa.edu")
as necessary.
Packages required but not available: 'modeest', 'tensorflow', 'keras'

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

Packages suggested but not available for checking: 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Deisy Morselli Gysi <deisy.ccnr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Deisy", "Morselli"),
                      family = "Gysi",
                      role = c("aut", "cre"),
                      email = "deisy.ccnr@gmail.com"),
               person(given = c("Tiago", "de", "Miranda"),
                      family = "Fragoso",
                      role = "aut"),
               person(given = "Eivind",
                      family = "Almaas",
                      role = "aut"),
               person(given = "Katja",
                      family = "Nowick.",
                      role = "aut"))
as necessary.

The Description field contains
  <arXiv:1802.00828>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘visNetwork’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'wTO'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Bill Venables <Bill.Venables@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bill",
                    family = "Venables",
                    role = c("aut", "cre"),
                    email = "bill.venables@gmail.com")
as necessary.
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/codingMatrices.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'devtools', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Zhiyong Zhang <johnnyzhz@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhiyong",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "johnnyzhz@gmail.com"),
               person(given = "Ke-Hai",
                      family = "Yuan",
                      role = "aut"))
as necessary.
Packages required but not available: 'dygraphs', 'plotly'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/coenocliner.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David W. Roberts <droberts@montana.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("David", "W."),
                    family = "Roberts",
                    role = c("aut", "cre"),
                    email = "droberts@montana.edu")
as necessary.
Packages required but not available: 'Hmisc', 'rhandsontable'

Packages suggested but not available for checking:
  'rmarkdown', 'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DR.SC', 'PRECAST', 'ProFAST', 'Seurat'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘config’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'visOmopResults', 'covr', 'DiagrammeR', 'DT', 'flextable', 'gt',
  'Hmisc', 'knitr', 'plotly', 'reactable', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'CirceR', 'covr', 'DiagrammeR', 'gt', 'knitr', 'rmarkdown',
  'SqlRender', 'visOmopResults'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'DatabaseConnector', 'ResultModelManager', 'SqlRender'

Packages suggested but not available for checking:
  'CirceR', 'Eunomia', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Elias Laurin Meyer <elias.meyer@meduniwien.ac.at>’

The Description field contains
  in Meyer et al. <arXiv:2202.02182>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DT'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown', 'gt', 'flextable', 'visOmopResults'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘CohortSurvival-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optionsTableSurvival
> ### Title: Additional arguments for the function tableSurvival()
> ### Aliases: optionsTableSurvival
> 
> ### ** Examples
> 
> {
+ optionsTableSurvival()
+ }
Error in loadNamespace(x) : there is no package called ‘visOmopResults’
Calls: optionsTableSurvival ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'visOmopResults', 'flextable', 'gt', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘DiagrammeR’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Wilmer Martinez <womartin@asu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Wilmer",
                    family = "Martinez",
                    role = c("aut", "cre"),
                    email = "womartin@asu.edu")
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘coincident_profile.Rd’:
    http://dx.doi.org/10.1016/j.spl.2015.11.008
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘utils.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Philipp Aschersleben <aschersleben@statistik.tu-dortmund.de>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘monitorCointegration.Rd’:
    http://dx.doi.org/10.2139/ssrn.2624657
  File ‘monitorStationarity.Rd’:
    http://dx.doi.org/10.2139/ssrn.2624657
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Philipp Aschersleben <aschersleben@statistik.tu-dortmund.de>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘cointReg.Rd’:
    http://dx.doi.org/10.2307/2297545
    http://dx.doi.org/10.2307/2298004
    http://dx.doi.org/10.1017/S0266466600004217
    http://dx.doi.org/10.2307/2951763
    http://dx.doi.org/10.1016/j.jeconom.2013.10.015
  File ‘cointRegD.Rd’:
    http://dx.doi.org/10.2307/2298004
    http://dx.doi.org/10.1017/S0266466600004217
    http://dx.doi.org/10.2307/2951763
  File ‘cointRegFM.Rd’:
    http://dx.doi.org/10.2307/2297545
  File ‘cointRegIM.Rd’:
    http://dx.doi.org/10.1016/j.jeconom.2013.10.015
  File ‘getBandwidth.Rd’:
    http://dx.doi.org/10.2307/2938229
    http://dx.doi.org/10.2307/2297912
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘M. Helena Goncalves <mhgoncal@ualg.pt>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("M.", "Helena"),
                      family = "Goncalves",
                      role = c("aut", "cre"),
                      email = "mhgoncal@ualg.pt"),
               person(given = c("M.", "Salome"),
                      family = "Cabral",
                      role = "aut"),
               person(given = c("apart", "from", "a", "set", "of", "Fortran-77", "subroutines", "written", "by", "R."),
                      family = "Piessens",
                      role = "aut"),
               person(given = "E.",
                      family = "de Doncker",
                      role = "aut"),
               person(given = c("belonging", "to", "the", "suite"),
                      family = "\"Quadpack\".",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Krishanu Mukherjee <toton1181@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Krishanu",
                    family = "Mukherjee",
                    role = c("aut", "cre"),
                    email = "toton1181@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Package which this enhances but not available for checking: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Nathan Levett <nathan.a.z.levett@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/Skenvy/Collatz/issues/new/choose
which should likely be
  https://github.com/Skenvy/Collatz/issues/new/choose/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'devtools', 'covr', 'DT', 'pkgdown', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Steve Condylios <steve.condylios@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Steve",
                    family = "Condylios",
                    role = c("aut", "cre"),
                    email = "steve.condylios@gmail.com",
                    comment = c(ORCID = "0000-0003-0599-844X"))
as necessary.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘collinear.R’ ‘cor_cramer_v.R’ ‘cor_df.R’ ‘cor_select.R’ ‘f_auc.Rd’
    ‘f_r2.Rd’ ‘f_r2_counts.Rd’ ‘f_v.Rd’ ‘f_v_rf_categorical.Rd’
    ‘identify.R’ ‘model_formula.R’ ‘preference_order.R’
    ‘preference_order_methods.R’ ‘target_encoding_methods.R’ ‘validate.R’
    ‘vif_df.R’ ‘vif_select.R’
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/collin.Rnw’
(Is a VignetteBuilder field missing?)

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Thiyanga Talagala <thiyanga.talagala@monash.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thiyanga",
                    family = "Talagala",
                    role = c("aut", "cre"),
                    email = "thiyanga.talagala@monash.edu")
as necessary.
Maintainer: ‘Hui Zhang <hzhang@northwestern.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jiahui",
                      family = "Xu",
                      role = "aut"),
               person(given = "Xueyan",
                      family = "Liu",
                      role = "aut"),
               person(given = "Lin",
                      family = "Li",
                      role = "aut"),
               person(given = "Cheng",
                      family = "Cheng",
                      role = "aut"),
               person(given = "Hui",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "hzhang@northwestern.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘config’

Packages suggested but not available for checking:
  'knitr', 'leaflet', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'pkgdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘simulate_populations.R’
Running examples in ‘colorednoise-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autocorr_sim
> ### Title: Simulate Temporally Autocorrelated Populations for Every
> ###   Combination of Parameters
> ### Aliases: autocorr_sim
> 
> ### ** Examples
> 
> survival_range <- autocorr_sim(timesteps = 30, start = 200, survPhi = 0.3, fecundPhi = 0.1,
+                                survMean = c(0.2, 0.3, 0.4, 0.5, 0.6), survSd = 0.5,
+                                fecundMean = 1.1, fecundSd = 0.5, replicates = 50)
Warning: `rerun()` was deprecated in purrr 1.0.0.
ℹ Please use `map()` instead.
  # Previously
  rerun(50, ., pmap(., unstructured_pop))

  # Now
  map(1:50, ~ list(., pmap(., unstructured_pop)))
ℹ The deprecated feature was likely used in the colorednoise package.
  Please report the issue at <https://github.com/japilo/colorednoise/issues>.
Warning: `cross_df()` was deprecated in purrr 1.0.0.
ℹ Please use `tidyr::expand_grid()` instead.
ℹ See <https://github.com/tidyverse/purrr/issues/768>.
ℹ The deprecated feature was likely used in the colorednoise package.
  Please report the issue at <https://github.com/japilo/colorednoise/issues>.
Error in cross_df(list(start = start, timesteps = timesteps, survPhi = survPhi,  : 
  The package "tibble" is required.
Calls: autocorr_sim ... eval_dots -> lapply -> FUN -> cross_df -> check_installed
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘quarto’

VignetteBuilder package required for checking but not installed: ‘quarto’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'plotly', 'knitr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Packages suggested but not available for checking:
  'rgl', 'zonohedra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/blueflame.rnw’
   ‘inst/doc/convexity.rnw’
   ‘inst/doc/emulation.rnw’
   ‘inst/doc/gallery.rnw’
   ‘inst/doc/inversion.rnw’
   ‘inst/doc/lens-aging.rnw’
   ‘inst/doc/optimals.rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Andrew Heiss <andrew@andrewheiss.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Alan Inglis <alan.n.inglis@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alan",
                    family = "Inglis",
                    role = c("aut", "cre"),
                    email = "alan.n.inglis@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rgl'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yang Ni <yni@stat.tamu.edu>’

The Description field contains
  categorical data. See Ni, Y. (2022) <arXiv:2209.08579> "Bivariate
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Maintainer: ‘Andreas Muehling <andreas.muehling@tum.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andreas",
                    family = "Muehling",
                    role = c("aut", "cre"),
                    email = "andreas.muehling@tum.de")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘DT’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools', 'plotly', 'quarto', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Minghui Wang <m.h.wang@live.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Minghui",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "m.h.wang@live.com"),
               person(given = "Yiyuan",
                      family = "Liu",
                      role = "aut"),
               person(given = "Shizhong",
                      family = "Han",
                      role = "aut"))
as necessary.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking:
  'MTS', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Breya McGlown <bswlker2@memphis.edu>’

The Description field contains
  Heard & Rubin-Delanchy (2017) <arXiv:1707.06897>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Problems with news in ‘NEWS.md’:
No news entries found.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Vince Carey <stvjc@channing.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Scott",
                      family = "Chasalow",
                      role = "aut"),
               person(given = "Vince",
                      family = "Carey",
                      role = "cre",
                      email = "stvjc@channing.harvard.edu"))
as necessary.
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) xsimplex.Rd:6: Lost braces; missing escapes or markup?
     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
Maintainer: ‘Florian Ziel <florian.ziel@uni-due.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Florian",
                    family = "Ziel",
                    role = c("aut", "cre"),
                    email = "florian.ziel@uni-due.de")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Seurat'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Benjamin Blonder <benjamin.blonder@berkeley.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Benjamin",
                    family = "Blonder",
                    role = c("aut", "cre"),
                    email = "benjamin.blonder@berkeley.edu")
as necessary.
checkRd: (-1) comet.Rd:20: height/width attributes should be in pixels
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
Package required but not available: ‘yaml’

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Antonio Canale <antonio.canale@unipd.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Antonio",
                      family = "Canale",
                      role = c("aut", "cre"),
                      email = "antonio.canale@unipd.it"),
               person(given = "Daniele",
                      family = "Durante",
                      role = "ctb"),
               person(given = "Arianna",
                      family = "Falcioni",
                      role = "aut"),
               person(given = "Luisa",
                      family = "Galtarossa",
                      role = "aut"),
               person(given = "Tommaso",
                      family = "Rigon",
                      role = "ctb"))
as necessary.
checkRd: (-1) BMD.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘leaflet’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) count_pairs.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_log_nonparam.Rd:36: Lost braces; missing escapes or markup?
    36 | {0, 1}.
       | ^
checkRd: (-1) score_log_semiparam.Rd:40: Lost braces; missing escapes or markup?
    40 | values in {0, 1}.
       |           ^
checkRd: (-1) sort_pairs.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'DatabaseConnector', 'SqlRender', 'rJava', 'rmarkdown'

Package suggested but not available for checking: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kornelius Rohmeyer <rohmeyer@small-projects.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kornelius",
                      family = "Rohmeyer",
                      role = c("aut", "cre"),
                      email = "rohmeyer@small-projects.de",
                      comment = c(ROR = "R package")),
               person(given = c("see", "COPYRIGHTS", "file", "for", "the", "authors", "of", "the", "java"),
                      family = "libraries",
                      role = "aut"))
as necessary.
Packages suggested but not available for checking: 'rJava', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/CommonJavaJars.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jia-Han Shih <tommy355097@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jia-Han",
                    family = "Shih",
                    role = c("aut", "cre"),
                    email = "tommy355097@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'rJava', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘wrassp’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ana C. Braga <acb@dps.uminho.pt>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ana", "C.", "Braga", "with", "contributions", "from", "Hugo"),
                      family = "Frade",
                      role = "aut"),
               person(given = "Sara",
                      family = "Carvalho",
                      role = "aut"),
               person(given = c("Andre", "M."),
                      family = "Santiago",
                      role = "aut"),
               person(given = c("Ana", "C."),
                      family = "Braga",
                      role = "cre",
                      email = "acb@dps.uminho.pt"))
as necessary.
Maintainer: ‘Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Christina",
                      family = "Heinze-Deml",
                      role = c("aut", "cre"),
                      email = "heinzedeml@stat.math.ethz.ch"),
               person(given = "Nicolai",
                      family = "Meinshausen",
                      role = "aut",
                      email = "meinshausen@stat.math.ethz.ch"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlTable’

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rmarkdown', 'knitr', 'kableExtra', 'flextable', 'rmdformats'

Packages suggested but not available for checking: 'shinyjqui', 'DT'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘compareMCMCs.R’ ‘metrics-addMetrics.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘CEEMDANML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Paul Murrell <p.murrell@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Paul",
                    family = "Murrell",
                    role = c("aut", "cre"),
                    email = "p.murrell@auckland.ac.nz")
as necessary.
checkRd: (-1) glass.Rd:10: Lost braces
    10 | \item{item}{factor}{200 levels - which item the measurements came from}
       |                    ^
checkRd: (-1) glass.Rd:11-12: Lost braces
    11 | \item{fragment}{factor}{4 levels - which of the four fragments from each item the observations were made
       |                        ^
checkRd: (-1) glass.Rd:13: Lost braces
    13 | \item{logNaO}{numeric}{log of sodium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:14: Lost braces
    14 | \item{logMgO}{numeric}{log of magnesium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:15: Lost braces
    15 | \item{logAlO}{numeric}{log of aluminium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:16: Lost braces
    16 | \item{logSiO}{numeric}{log of silicon concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:17: Lost braces
    17 | \item{logKO}{numeric}{log of potassium concentration to oxygen concentration}
       |                      ^
checkRd: (-1) glass.Rd:18: Lost braces
    18 | \item{logCaO}{numeric}{log of calcium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:19: Lost braces
    19 | \item{logFeO}{numeric}{log of iron concentration to oxygen concentration}
       |                       ^
Maintainer: ‘Samuel W.K. Wong <samuel.wong@uwaterloo.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Samuel", "W.K."),
                      family = "Wong",
                      role = c("aut", "cre"),
                      email = "samuel.wong@uwaterloo.ca"),
               person(given = "Dylan",
                      family = "Shi",
                      role = "aut"),
               person(given = "Megan",
                      family = "Hazlett",
                      role = "aut"),
               person(given = "Jasmine",
                      family = "Cheng",
                      role = "aut"))
as necessary.
checkRd: (-1) atomdeps.Rd:9: Lost braces
     9 |  \item{"tangle"}: {Dihedral angle defined by atoms A-B-C-D as described below. \code{NA}'s represent the free side chain dihedral angles \emph{chi} for that amino acid.}
       |                   ^
checkRd: (-1) atomdeps.Rd:10: Lost braces; missing escapes or markup?
    10 |  \item{"names"}: {The component atoms of the amino acid side chain.  Represents atom D in the dihedral.}
       |                  ^
checkRd: (-1) atomdeps.Rd:11: Lost braces; missing escapes or markup?
    11 |  \item{"matx"}: {The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".}
       |                 ^
checkRd: (-1) atomdeps.Rd:12: Lost braces; missing escapes or markup?
    12 |  \item{"bangle"}: {Planar bond angle formed between B-C-D}
       |                   ^
checkRd: (-1) atomdeps.Rd:13: Lost braces; missing escapes or markup?
    13 |  \item{"blength"}: {Bond length between C-D}
       |                    ^
Maintainer: ‘Saralees Nadarajah <Saralees.Nadarajah@manchester.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Martin",
                      family = "Wiegand",
                      role = "aut"),
               person(given = "Saralees",
                      family = "Nadarajah",
                      role = c("aut", "cre"),
                      email = "saralees.nadarajah@manchester.ac.uk"))
as necessary.
Package required but not available: ‘fExtremes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) keener.Rd:82: Lost braces; missing escapes or markup?
    82 | a_{ij} = (S_ij + 1) / (S_ij + S_ji + 2). This step should make comparing
       |   ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rhandsontable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'DT', 'networkD3'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘M. A. J. Zondervan-Zwijnenburg <m.zondervan@vilans.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("M.", "A.", "J."),
                    family = "Zondervan-Zwijnenburg",
                    role = c("aut", "cre"),
                    email = "m.zondervan@vilans.nl")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Albert Dorador <albert.dorador@estudiant.upc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Albert",
                      family = "Dorador",
                      role = c("aut", "cre"),
                      email = "albert.dorador@estudiant.upc.edu"),
               person(given = c("Uffe", "Høgsbro"),
                      family = "Thygesen",
                      role = "aut"))
as necessary.
Maintainer: ‘Michał Krassowski <krassowski.michal+r@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'SuperLearner', 'gWQS', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tony Pourmohamad <tpourmohamad@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Andrew Raim <andrew.raim@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Kimberly", "Sellers", "Thomas", "Lotze", "<thomas.lotze@thomaslotze.com>", "Andrew", "Raim"),
                      family = "<andrew.raim@gmail.com>",
                      role = "aut",
                      email = "andrew.raim@gmail.com"),
               person(given = "Andrew",
                      family = "Raim",
                      role = "cre",
                      email = "andrew.raim@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'Compositional', 'factoextra'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rgl', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Zengchao Hao <z.hao4univ@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Zengchao",
                    family = "Hao",
                    role = c("aut", "cre"),
                    email = "z.hao4univ@gmail.com")
as necessary.
Maintainer: ‘Bowen Liu <bowen.liu@umkc.edu>’

The Description field contains
  found in Bowen Liu, Malwane M.A. Ananda (2023) <arXiv:2309.16443>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michel Semenou <michel.semenou@oniris-nantes.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michel",
                    family = "Semenou",
                    role = c("aut", "cre"),
                    email = "michel.semenou@oniris-nantes.fr")
as necessary.
Maintainer: ‘AC Del Re <acdelre@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("AC", "Del"),
                    family = "Re",
                    role = c("aut", "cre"),
                    email = "acdelre@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Zoltan Botta-Dukat <botta-dukat.zoltan@okologia.mta.hu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Zoltan",
                    family = "Botta-Dukat",
                    role = c("aut", "cre"),
                    email = "botta-dukat.zoltan@okologia.mta.hu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Zhicheng Du <dgdzc@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhicheng",
                      family = "Du",
                      role = c("aut", "cre"),
                      email = "dgdzc@hotmail.com"),
               person(given = "Ziqiang",
                      family = "Lin",
                      role = "aut"),
               person(given = "Yuantao",
                      family = "Hao",
                      role = "aut"))
as necessary.
Maintainer: ‘Mark Baas <mark.baas@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mark",
                    family = "Baas",
                    role = c("aut", "cre"),
                    email = "mark.baas@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'DT', 'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Adrienne Traxler <adrienne.traxler@wright.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'devtools', 'kableExtra', 'covr'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
checkRd: (-1) concstats_hhi.Rd:13: Lost braces; missing escapes or markup?
    13 | value is required. Ranges from {0, 1} and often used for comparison over
       |                                ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'quarto'

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DiagrammeR'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'htmlTable', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David Clement <dyc24@cornell.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Clement",
                    role = c("aut", "cre"),
                    email = "dyc24@cornell.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Christina",
                      family = "Heinze-Deml",
                      role = c("aut", "cre"),
                      email = "heinzedeml@stat.math.ethz.ch"),
               person(given = "Jonas",
                      family = "Peters",
                      role = "aut",
                      email = "jonas.peters@math.ku.dk"),
               person(given = c("Asbjoern", "Marco", "Sinius"),
                      family = "Munk",
                      role = "aut",
                      email = "fgp998@alumni.ku.dk"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Description field contains
  <arXiv:1202.3775>), Residual Prediction test (based on Shah and
  Buehlmann, <arXiv:1511.03334>), Invariant environment prediction,
  <arXiv:1706.08576>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                      ^
checkRd: (-1) KCI.Rd:44: Lost braces; missing escapes or markup?
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                                    ^
Package required but not available: ‘knitr’

Packages suggested but not available for checking: 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Scott Chamberlain <myrmecocystus@gmail.com>’

Found the following (possibly) invalid file URI:
  URI: CODE_OF_CONDUCT.md
    From: README.md
Maintainer: ‘Marta Sestelo <sestelo@uvigo.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Luis",
                      family = "Meira-Machado",
                      role = "aut"),
               person(given = "Marta",
                      family = "Sestelo",
                      role = c("aut", "cre"),
                      email = "sestelo@uvigo.es"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
No news entries found.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > shinytest2::test_app()
  Error in loadNamespace(x) : there is no package called 'shinytest2'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'scagnostics', 'keras', 'bartMachine'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
'library' or 'require' call not declared from: ‘e1071’
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'ecospat', 'ENMeval'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Bill Venables <Bill.Venables@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bill",
                    family = "Venables",
                    role = c("aut", "cre"),
                    email = "bill.venables@gmail.com")
as necessary.
Package required but not available: ‘rgl’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/confidence.Rnw’
(Is a VignetteBuilder field missing?)

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mathias Fuchs<mathias@mathiasfuchs.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mathias",
                    family = "Fuchs",
                    role = c("aut", "cre"),
                    email = "mathias@mathiasfuchs.de")
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘confIntVariance-package.Rd’:
    \keyword{variance, confidence interval}
Packages required but not available: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'DiagrammeR'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'rstanarm', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Niharika Gauraha <niharika.gauraha@farmbio.uu.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Niharika",
                      family = "Gauraha",
                      role = c("aut", "cre"),
                      email = "niharika.gauraha@farmbio.uu.se"),
               person(given = "Ola",
                      family = "Spjuth",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Paolo Vergottini <paolo.vergottini@gmail.com>’

The Description field contains
  Fontana, and Vantini (2021) <arXiv:2102.06746>, Diquigiovanni, Fontana,
  and Vantini (2021) <arXiv:2106.01792>, Solari, and Djordjilovic (2021)
  <arXiv:2103.00627>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Running examples in ‘conformalInference.fd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: conformal.fun.jackplus
> ### Title: Functional Jackknife + Prediction Regions
> ### Aliases: conformal.fun.jackplus
> 
> ### ** Examples
> 
> library(roahd)
Error in library(roahd) : there is no package called ‘roahd’
Execution halted
Maintainer: ‘Yachong Yang <yachong@wharton.upenn.edu>’

The Description field contains
  <arxiv:2104.13871>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jesse Hemerik <j.b.a.hemerik@lumc.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jesse",
                      family = "Hemerik",
                      role = c("aut", "cre"),
                      email = "j.b.a.hemerik@lumc.nl"),
               person(given = "Jelle",
                      family = "Goeman",
                      role = "aut"))
as necessary.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) binary_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'bookdown', 'knitr', 'rmarkdown', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘James Conigrave <james.conigrave@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "James",
                    family = "Conigrave",
                    role = c("aut", "cre"),
                    email = "james.conigrave@gmail.com")
as necessary.
Maintainer: ‘José Manuel Monroy Kuhn <nolozz@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sidharth Macherla <msidharthrasik@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'Hmisc', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'rsconnect', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘frequencyConnectedness’

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘pins’

Package suggested but not available for checking: ‘covr’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'whirl'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling', 'usethis', 'whirl'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'covr', 'lintr'

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

Packages suggested but not available for checking:
  'knitr', 'lintr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David M. Kaplan <dmkaplan2000@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("David", "M."),
                      family = "Kaplan",
                      role = c("cre", "aut"),
                      email = "dmkaplan2000@gmail.com"),
               person(given = "Marco",
                      family = "Andrello",
                      role = "ctb",
                      email = "marco.andrello@gmail.com"))
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘chile.loco.Rd’:
    http://dx.doi.org/10.1016/j.pocean.2014.03.011
  File ‘damselfish.lods.Rd’:
    http://dx.doi.org/10.1046/j.1471-8286.2003.00439.x
Maintainer: ‘Jonas Moss <jonas.gjertsen@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘conogive.Rd’:
    https://doi.org/10.1007/978-1-4757-2691-6_15
Packages required but not available: 'leidenAlg', 'sccore'

Packages suggested but not available for checking:
  'conosPanel', 'knitr', 'p2data', 'pagoda2', 'rmarkdown', 'Seurat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Alexis Dinno <alexis.dinno@pdx.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexis",
                    family = "Dinno",
                    role = c("aut", "cre"),
                    email = "alexis.dinno@pdx.edu")
as necessary.
Package required but not available: ‘kableExtra’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'plotly', 'DT'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘api-get_datalog.R’ ‘api-get_device.R’ ‘api-get_devices.R’
    ‘api-get_element.R’ ‘api-get_elements.R’ ‘api-get_project.R’
    ‘api-get_projects.R’ ‘api-get_users_me.R’ ‘client.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'DiagrammeR', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mary C Meyer <meyer@stat.colostate.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Mary", "C"),
                    family = "Meyer",
                    role = c("aut", "cre"),
                    email = "meyer@stat.colostate.edu")
as necessary.
Packages required but not available: 'ConsRank', 'rlist', 'smacof'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Josep Puig <puigjos@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Josep", "Puig"),
                      family = "Sallés",
                      role = "aut"),
               person(given = "Josep",
                      family = "Puig",
                      role = "cre",
                      email = "puigjos@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'DiagrammeR', 'knitr', 'reprex', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Angelo Mazza <a.mazza@unict.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Antonio",
                      family = "Punzo",
                      role = "aut"),
               person(given = "Angelo",
                      family = "Mazza",
                      role = c("aut", "cre"),
                      email = "a.mazza@unict.it"),
               person(given = c("Paul", "D."),
                      family = "McNicholas",
                      role = "aut"))
as necessary.
Package required but not available: ‘visNetwork’

Packages suggested but not available for checking:
  'knitr', 'plotly', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘quanteda’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Robin K. S. Hankin <hankin.robin@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Robin", "K.", "S."),
                    family = "Hankin",
                    role = c("aut", "cre"),
                    email = "hankin.robin@gmail.com")
as necessary.
Maintainer: ‘Carl Witthoft <cellocgw@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Carl",
                    family = "Witthoft",
                    role = c("aut", "cre"),
                    email = "cellocgw@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Nicholas Hamilton <n.hamilton@unsw.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nicholas",
                    family = "Hamilton",
                    role = c("aut", "cre"),
                    email = "n.hamilton@unsw.edu.au")
as necessary.
Specified C++11: support will be removed soon
checkRd: (-1) getConvexHull.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:30: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘rmarkdown’

Packages suggested but not available for checking: 'covr', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tony Murphy <tonymurphy55.am@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tony",
                    family = "Murphy",
                    role = c("aut", "cre"),
                    email = "tonymurphy55.am@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'roxygen2', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rms’

Packages suggested but not available for checking:
  'knitr', 'kableExtra', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'devtools', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Zijian Guo <zijguo@stat.rutgers.edu>’

The Description field contains
  when the model is known ('Guo and Small' (2016) <arXiv:1602.01051>) and
  <arXiv:2010.09922>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘orthoDr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ben C. Ubah <ubah.ben22@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Ben", "C."),
                    family = "Ubah",
                    role = c("aut", "cre"),
                    email = "ubah.ben22@gmail.com")
as necessary.
Maintainer: ‘Eric S. Kawaguchi <erickawaguchi@ucla.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Eric", "S."),
                    family = "Kawaguchi",
                    role = c("aut", "cre"),
                    email = "erickawaguchi@ucla.edu")
as necessary.
Package required but not available: ‘riskRegression’

Packages suggested but not available for checking:
  'pammtools', 'plotly', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘SHELF’

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Pierre Lafaye De Micheaux <lafaye@unsw.edu.au>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'cmdstanr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rmarkdown', 'leaflet'

Packages suggested but not available for checking:
  'devtools', 'formattable', 'knitr', 'kableExtra', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘RWeka’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gordon Shotwell <g.e.shotwell@gmail.com>’

Found the following (possibly) invalid file URI:
  URI: CONDUCT.md
    From: README.md
Package required but not available: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Specified C++11: support will be removed soon
Running examples in ‘cooltools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kde2
> ### Title: Multi-dimensional adaptive kernel density estimation
> ### Aliases: kde2
> 
> ### ** Examples
> 
> # make a mock sample of n d-dimensional points from
> # three different components (1D line, 2D square, d-D normal distr)
> d = 3 # number of dimensions of mock point set; try to choose different values 2, 3, 4, ...
> n = 1e4 # number of particles per component
> set.seed(1)
> x = rbind(cbind(array(rep(runif(n,-1,1),2),c(n,2)),array(0,c(n,d-2))),
+           cbind(array(runif(2*n),c(n,2)),array(0,c(n,d-2))),
+           array(rnorm(d*n),c(n,d)))
> 
> # grid total projected probability density
> npixels = 500 # number of pixels along a grid side
> q = midseq(-3,3,npixels)
> f1 = outer(dnorm(q),dnorm(q),'*')/3+outer(dunif(q),dunif(q),'*')/3
> q = seq(round(npixels/3),round(npixels*2/3))
> f1[q+npixels*(q-1)] = f1[q+npixels*(q-1)]+(npixels/6)^2/length(q)/3
> 
> # recover 2D projected pdf from 3D point sample using different methods
> f2 = kde2(x, n=npixels, xlim=c(-3,3), ylim=c(-3,3), algorithm='basic', probability=TRUE)$field
> f3 = kde2(x, n=npixels, xlim=c(-3,3), ylim=c(-3,3), algorithm='kdefast', probability=TRUE)$field
> f4 = kde2(x, n=npixels, xlim=c(-3,3), ylim=c(-3,3), algorithm='kdenn', probability=TRUE)$field
Error in kde2(x, n = npixels, xlim = c(-3, 3), ylim = c(-3, 3), algorithm = "kdenn",  : 
  Package EBImage is needed to run kde2 in with kdenn or manual algorithm.
Execution halted
Maintainer: ‘Jochen Staudacher <jochen.staudacher@hs-kempten.de>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rgl'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Drew Schmidt <wrathematics@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘John Hughes <drjphughesjr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Emily",
                      family = "Goren",
                      role = "aut",
                      email = "emily.goren@gmail.com"),
               person(given = "John",
                      family = "Hughes",
                      role = c("aut", "cre"),
                      email = "drjphughesjr@gmail.com"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |            ^
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |                          ^
Maintainer: ‘Fuyuan David Li <LFY@gwmail.gwu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Fuyuan", "David"),
                    family = "Li",
                    role = c("aut", "cre"),
                    email = "lfy@gwmail.gwu.edu")
as necessary.
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                          ^
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                                      ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                  ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                              ^
Maintainer: ‘MA Jian <majian03@gmail.com>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘construct_empirical_copula.Rd’:
    \keyword{empirical copula; rank}
  File ‘entknn.Rd’:
    \keyword{entropy; kNN}
checkRd: (-1) ComputeCope.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:57-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DrawContour.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Draws the contour {f=c}.}
       |                          ^
checkRd: (-1) DrawContour.Rd:20: Lost braces; missing escapes or markup?
    20 | Draws the contour {f=c}.
       |                   ^
checkRd: (-1) cope.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:35: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'fitbitViz', 'mapview'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘leaflet’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'smacofx', 'smacof'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Simon Boge Brant <simbrant91@gmail.com>’

The Description field contains
  via gradient boosting [Brant, Hobæk Haff (2022); <arXiv:2208.04669>].
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Bouchra R. Nasri <bouchra.nasri@umontreal.ca>’

The Description field contains
  <arXiv:2301.13408>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Takeshi Emura <takeshiemura@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Takeshi",
                      family = "Emura",
                      role = c("aut", "cre"),
                      email = "takeshiemura@gmail.com"),
               person(given = "Xinwei",
                      family = "Huang",
                      role = "aut"),
               person(given = "Ting-Hsuan",
                      family = "Long",
                      role = "aut"),
               person(given = "Li-Hsien",
                      family = "Sun",
                      role = "aut"))
as necessary.
Maintainer: ‘Xin-Wei Huang <xinweihuang@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xin-Wei",
                      family = "Huang",
                      role = c("aut", "cre"),
                      email = "xinweihuang@hotmail.com"),
               person(given = "Takeshi",
                      family = "Emura",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'Ball'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Lei Yang <leiyangslu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Lei",
                    family = "Yang",
                    role = c("aut", "cre"),
                    email = "leiyangslu@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Shuang Song <song-s19@mails.tsinghua.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wei",
                      family = "Jiang",
                      role = "aut"),
               person(given = "Shuang",
                      family = "Song",
                      role = c("aut", "cre"),
                      email = "song-s19@mails.tsinghua.edu.cn"),
               person(given = "Lin",
                      family = "Hou",
                      role = "aut"),
               person(given = "Hongyu",
                      family = "Zhao",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Andrei Boutyline <aboutyl@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andrei",
                    family = "Boutyline",
                    role = c("aut", "cre"),
                    email = "aboutyl@umich.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) getSurface.Rd:22: Lost braces
    22 | value \code{getSurface} shortens the output of \code{conv} to remove artificial surface layers. The output is thus a subset of the input, and identical in structure to the /code{conv} output.
       |                                                                                                                                                                                  ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'gt', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'SRS', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Taylor Arnold <tarnold2@richmond.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Taylor",
                      family = "Arnold",
                      role = c("aut", "cre"),
                      email = "tarnold2@richmond.edu"),
               person(given = "Lauren",
                      family = "Tilton",
                      role = "aut"))
as necessary.
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Guoli Sun <guolisun87@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alex",
                      family = "Krasnitz",
                      role = "aut"),
               person(given = "Guoli",
                      family = "Sun",
                      role = c("aut", "cre"),
                      email = "guolisun87@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Santhosh Sasanapuri <santhosh458@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Navin",
                      family = "Loganathan",
                      role = "aut"),
               person(given = "Mohan",
                      family = "Manivannan",
                      role = "aut"),
               person(given = "Santhosh",
                      family = "Sasanapuri",
                      role = c("aut", "cre"),
                      email = "santhosh458@gmail.com"),
               person(given = "LatentView",
                      family = "Analytics",
                      role = "ctb"))
as necessary.
Maintainer: ‘John Ferguson <john.ferguson@nuigalway.ie>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘linkd.Rd’:
    \keyword{Feligi/Sunter,}
    \keyword{algorithm,}
    \keyword{class,}
    \keyword{linkage,}
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Niklas Pfister <np@math.ku.dk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Niklas",
                      family = "Pfister",
                      role = c("aut", "cre"),
                      email = "np@math.ku.dk"),
               person(given = "Sebastian",
                      family = "Weichwald",
                      role = "aut"))
as necessary.
Package required but not available: ‘devtools’

Packages suggested but not available for checking:
  'DT', 'knitr', 'plotly', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Korbinian Strimmer <strimmerlab@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Juliane",
                      family = "Schafer",
                      role = "aut"),
               person(given = "Rainer",
                      family = "Opgen-Rhein",
                      role = "aut"),
               person(given = "Verena",
                      family = "Zuber",
                      role = "aut"),
               person(given = "Miika",
                      family = "Ahdesmaki",
                      role = "aut"),
               person(given = c("A.", "Pedro", "Duarte"),
                      family = "Silva",
                      role = "aut"),
               person(given = "Korbinian",
                      family = "Strimmer.",
                      role = "aut"),
               person(given = "Korbinian",
                      family = "Strimmer",
                      role = "cre",
                      email = "strimmerlab@gmail.com"))
as necessary.
Package required but not available: ‘knitr’

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

Package suggested but not available for checking: ‘shinytest2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'quanteda', 'RNewsflow'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Prabina Kumar Meher <meherprabin@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Prabina", "Kumar", "Meher", "&", "A.", "R."),
                      family = "Rao",
                      role = "aut"),
               person(given = c("Prabina", "Kumar"),
                      family = "Meher",
                      role = "cre",
                      email = "meherprabin@yahoo.com"))
as necessary.
Maintainer: ‘Weiliang Qiu <stwxq@channing.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bernard",
                      family = "Rosner",
                      role = "aut"),
               person(given = "Shelley",
                      family = "Tworoger",
                      role = "aut"),
               person(given = "Weiliang",
                      family = "Qiu",
                      role = c("aut", "cre"),
                      email = "stwxq@channing.harvard.edu"))
as necessary.
Maintainer: ‘Abbas Rahal <Abbas.Rahal13@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Abbas",
                      family = "Rahal",
                      role = c("aut", "cre"),
                      email = "abbas.rahal13@gmail.com"),
               person(given = "Anna",
                      family = "Akpawu",
                      role = "aut"),
               person(given = "Justin",
                      family = "Chitpin",
                      role = "aut"),
               person(given = c("David", "R."),
                      family = "Bickel",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling', 'xcms'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pkgdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'gt', 'Hmisc', 'knitr', 'rmarkdown', 'rstanarm'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gary Witt <gary.witt@temple.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chris",
                      family = "Rohlfs",
                      role = "aut"),
               person(given = "Gary",
                      family = "Witt",
                      role = c("aut", "cre"),
                      email = "gary.witt@temple.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'BiocStyle', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Wim Van der Elst <Wim.vanderelst@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wim",
                      family = "Van der Elst",
                      role = c("aut", "cre"),
                      email = "wim.vanderelst@gmail.com"),
               person(given = "Geert",
                      family = "Molenberghs",
                      role = "aut"),
               person(given = "Dieter",
                      family = "Hilgers",
                      role = "aut"),
               person(given = c("&", "Nicole"),
                      family = "Heussen",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘corrRect.hclust.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'sparklyr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'WGCNA', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael G. Campana <campanam@si.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Michael", "G."),
                    family = "Campana",
                    role = c("aut", "cre"),
                    email = "campanam@si.edu")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.

The BugReports field in DESCRIPTION has
  https://github.com/campanam/rCorrSieve
which should likely be
  https://github.com/campanam/rCorrSieve/issues
instead.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ran Gao <rgao8@uic.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rawan",
                      family = "Allozi",
                      role = "aut"),
               person(given = "Hakan",
                      family = "Demirtas",
                      role = "aut"),
               person(given = "Ran",
                      family = "Gao",
                      role = c("aut", "cre"),
                      email = "rgao8@uic.edu"))
as necessary.
Maintainer: ‘Alan Inglis <alan.n.inglis@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alan",
                    family = "Inglis",
                    role = c("aut", "cre"),
                    email = "alan.n.inglis@gmail.com")
as necessary.
Packages required but not available: 'visNetwork', 'plotly'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Fran Urbano <viraltux@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Fran",
                    family = "Urbano",
                    role = c("aut", "cre"),
                    email = "viraltux@gmail.com")
as necessary.
Maintainer: ‘Danyang Yu <dyu33@jhu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Danyang",
                      family = "Yu",
                      role = c("aut", "cre"),
                      email = "dyu33@jhu.edu"),
               person(given = "Weiliang",
                      family = "Qiu",
                      role = "aut"),
               person(given = "Zeyu",
                      family = "Zhang",
                      role = "aut"),
               person(given = "Kimberly",
                      family = "Glass",
                      role = "aut"),
               person(given = "Jessica",
                      family = "Su",
                      role = "aut"),
               person(given = c("Dawn", "L."),
                      family = "DeMeo",
                      role = "aut"),
               person(given = "Kelan",
                      family = "Tantisira",
                      role = "aut"),
               person(given = c("Scott", "T."),
                      family = "Weiss",
                      role = "aut"))
as necessary.
Packages required but not available: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Augustin Mutak <mutak94@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Augustin",
                    family = "Mutak",
                    role = c("aut", "cre"),
                    email = "mutak94@gmail.com")
as necessary.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Michael Sachs <sachsmc@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Sachs",
                    role = c("aut", "cre"),
                    email = "sachsmc@gmail.com")
as necessary.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Andrew Harris <harris@astro.umd.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andrew",
                    family = "Harris",
                    role = c("aut", "cre"),
                    email = "harris@astro.umd.edu")
as necessary.
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'usethis', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yanlin Tang <yanlintang2018@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yanlin",
                      family = "Tang",
                      role = c("aut", "cre"),
                      email = "yanlintang2018@163.com"),
               person(given = c("Huixia", "Judy"),
                      family = "Wang",
                      role = "aut"))
as necessary.
Maintainer: ‘David Cortes <david.cortes.rivera@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Cortes",
                    role = c("aut", "cre"),
                    email = "david.cortes.rivera@gmail.com")
as necessary.
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/cotram.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘A. Christian Silva <a.christian.silva@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("A.", "Christian"),
                    family = "Silva",
                    role = c("aut", "cre"),
                    email = "a.christian.silva@gmail.com")
as necessary.
Package required but not available: ‘colordistance’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ivan Fernandez-Val <ivanf@bu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mingli",
                      family = "Chen",
                      role = "aut"),
               person(given = "Victor",
                      family = "Chernozhukov",
                      role = "aut"),
               person(given = "Ivan",
                      family = "Fernandez-Val",
                      role = c("aut", "cre"),
                      email = "ivanf@bu.edu"),
               person(given = "Blaise",
                      family = "Melly",
                      role = "aut"))
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'DT', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kellie Archer <archer.43@osu.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Timo Adam <timo.adam@uni-bielefeld.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Timo",
                    family = "Adam",
                    role = c("aut", "cre"),
                    email = "timo.adam@uni-bielefeld.de")
as necessary.

The Description field contains
  Hidden Markov Models for Time Series of Counts. <arXiv:1901.03275>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘psRes.Rd’:
    https://doi.org/10.1201/b20790
  File ‘stateDec.Rd’:
    https://doi.org/10.1201/b20790
Running examples in ‘countland-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cluster
> ### Title: Perform spectral clustering on dot products.
> ### Aliases: Cluster
> 
> ### ** Examples
> 
> gold_path <- system.file("testdata", package = "countland", mustWork = TRUE)
> gold.data <- Seurat::Read10X(data.dir = gold_path)
Error in loadNamespace(x) : there is no package called ‘Seurat’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Countr.Rcheck/00install.out’ for details.
Maintainer: ‘David M. Smith <dmccsmith@verizon.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("David", "M"),
                      family = "Smith",
                      role = "aut"),
               person(given = c("Malcolm", "J"),
                      family = "Faddy",
                      role = "aut"),
               person(given = c("David", "M."),
                      family = "Smith",
                      role = "cre",
                      email = "dmccsmith@verizon.net"))
as necessary.
Maintainer: ‘Anna Neufeld <aneufeld@fredhutch.org>’

The Description field contains
  <arXiv:2307.12985>. Intended for turning a matrix of single-cell RNA
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Brian King <brianking387@gmail.com>’

The Description field contains
  King and Kowal (2022) <arXiv:2110.14790>, and Kowal and Wu (2023)
  <arXiv:2110.12316>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tanujit Chakraborty <tanujitisi@gmail.com>’

The Description field contains
  is based on the algorithms by Liu et al. (2023) <arXiv:2311.14359>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available: 'ggformula', 'mosaic'

Package suggested but not available for checking: ‘usethis’

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

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

Packages suggested but not available for checking:
  'table1', 'knitr', 'rmarkdown', 'plotly', 'ggpmisc'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael Kirchner <michael@kirchner.io>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Kirchner",
                    role = c("aut", "cre"),
                    email = "michael@kirchner.io")
as necessary.
Found the following files/directories:
  ‘covfefe_inauguration.txt’
Maintainer: ‘Marcelo Ponce <m.ponce@utoronto.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marcelo",
                      family = "Ponce",
                      role = c("aut", "cre"),
                      email = "m.ponce@utoronto.ca"),
               person(given = "Amit",
                      family = "Sandhel",
                      role = "ctb"))
as necessary.
Packages required but not available:
  'plotly', 'htmlwidgets', 'DT', 'collapsibleTree'

Packages suggested but not available for checking:
  'knitr', 'devtools', 'roxygen2', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DT', 'networkD3'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Max Salvatore <mmsalva@umich.edu>’

Found the following (possibly) invalid file URI:
  URI: twitter.com/MaxSalTweets
    From: README.md
Package required but not available: ‘gt’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘pins’

Packages suggested but not available for checking:
  'covr', 'ggformula', 'ggstream', 'rmarkdown', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘usethis’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Peter Hoff <peter.hoff@duke.edu>’

The Description field contains
  McCormack and Zhang (2022) <arXiv:2207.12484> "Core Shrinkage
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Hana Sevcikova <hanas@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Naisyin",
                      family = "Wang",
                      role = "aut",
                      email = "nwangaa@umich.edu"),
               person(given = c("Adrian", "Raftery", "with", "contributions", "from", "Chris", "Fraley"),
                      family = "<fraley@uw.edu>",
                      role = "aut",
                      email = "fraley@uw.edu"),
               person(given = "Hana",
                      family = "Sevcikova",
                      role = "cre",
                      email = "hanas@uw.edu"))
as necessary.
Package required but not available: ‘yaml’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DT', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Shahin Tavakoli <s.tavakoli@warwick.ac.uk>’

The Description field contains
  <https://projecteuclid.org/euclid.aos/1498636862> <arXiv:1505.02023>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ben Barnard <ben_barnard@outlook.com>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘covTestR-package.Rd’:
    http://doi.org/10.1016/j.csda.2007.03.004
    http://doi.org/10.1016/j.jmva.2010.07.004
  File ‘homogeneityStatistics.Rd’:
    http://doi.org/10.1080/15598608.2017.1308895
    http://doi.org/10.3923/jas.2013.270.277
    http://doi.org/10.1016/j.jspi.2015.10.007
    http://doi.org/10.1016/S0378-3758(00)00209-3
    http://doi.org/10.1016/j.csda.2007.03.004
    http://doi.org/10.1016/j.jmva.2014.06.003
    http://doi.org/10.1016/j.jmva.2009.12.010
  File ‘structureStatistics.Rd’:
    http://doi.org/10.1080/00949655.2014.948441
    http://doi.org/10.1198/jasa.2010.tm09560
    http://doi.org/10.1016/j.jspi.2011.07.019
    http://doi.org/10.1214/aos/1031689018
    http://doi.org/10.14490/jjss.35.251
    http://doi.org/10.1016/j.jmva.2011.03.003
Specified C++11: support will be removed soon
Package required but not available: ‘shapes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘covtracer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: test_srcrefs
> ### Title: Extract test srcref objects
> ### Aliases: test_srcrefs test_srcrefs.coverage
> 
> ### ** Examples
> 
> options(covr.record_tests = TRUE)
> pkg_path <- system.file("examplepkg", package = "covtracer")
> cov <- covr::package_coverage(pkg_path)
Error in loadNamespace(x) : there is no package called ‘covr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [8s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(covtracer)
  > 
  > test_check("covtracer")
  ℹ Installing test packages
    • examplepkg (derived `examplepkg_cov`, `examplepkg_ns`)
  Error in   `source_dir()`:
    ! Failed to evaluate './setup_test_packages.R'.
  Caused by error in   `loadNamespace()`:
  ! there is no package called 'covr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("covtracer")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::assign(paste0(pkg, "_cov"), covr::package_coverage(pkg_dir)) at ./setup_test_packages.R:56:5
   15. ├─base::loadNamespace(x)
   16. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   17. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   18. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   19. │ └─base::stop(cond)
   20. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   21.   └─cli::cli_abort(...)
   22.     └─rlang::abort(...)
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'plotly', 'gt'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘randomForestSRC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Error(s) in re-building vignettes:
  ...
--- re-building ‘coxme.Rnw’ using Sweave
Loading required package: survival
Loading required package: bdsmatrix

Attaching package: ‘bdsmatrix’

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

    backsolve


Error: processing vignette 'coxme.Rnw' failed with diagnostics:
 chunk 6 
Error in library(kinship2) : there is no package called ‘kinship2’

--- failed re-building ‘coxme.Rnw’

--- re-building ‘laplace.Rnw’ using Sweave
Loading required package: survival
Loading required package: bdsmatrix

Attaching package: ‘bdsmatrix’

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

    backsolve

--- finished re-building ‘laplace.Rnw’

--- re-building ‘lmekin.Rnw’ using Sweave
Loading required package: survival
Loading required package: bdsmatrix

Attaching package: ‘bdsmatrix’

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

    backsolve

Loading required package: nlme
Loading required package: kinship2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘kinship2’

Error: processing vignette 'lmekin.Rnw' failed with diagnostics:
 chunk 4 (label = gaw) 
Error in pedigree(id, father, mother, sex = sex, famid = famid) : 
  could not find function "pedigree"

--- failed re-building ‘lmekin.Rnw’

--- re-building ‘variance.Rnw’ using Sweave
Loading required package: coxme
Loading required package: survival
Loading required package: bdsmatrix

Attaching package: ‘bdsmatrix’

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

    backsolve

--- finished re-building ‘variance.Rnw’

SUMMARY: processing the following files failed:
  ‘coxme.Rnw’ ‘lmekin.Rnw’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘coxphf-tidiers.R’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Hyeri You <h2you@health.ucsd.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hyeri",
                      family = "You",
                      role = c("aut", "cre"),
                      email = "h2you@health.ucsd.edu"),
               person(given = "Ronghui",
                      family = "Xu",
                      role = "aut"))
as necessary.
Maintainer: ‘Bella Vakulenko-Lagun <bella.vakulenko-lagun@mail.huji.ac.il>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bella",
                      family = "Vakulenko-Lagun",
                      role = c("aut", "cre"),
                      email = "bella.vakulenko-lagun@mail.huji.ac.il"),
               person(given = "Micha",
                      family = "Mandel",
                      role = "aut"),
               person(given = c("Rebecca", "A."),
                      family = "Betensky",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
checkRd: (-1) coxph.RT.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:59-71: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Quentin Giai Gianetto <quentin2g@yahoo.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Quentin", "Giai"),
                      family = "Gianetto",
                      role = c("aut", "cre"),
                      email = "quentin2g@yahoo.fr"),
               person(given = "Florence",
                      family = "Combes",
                      role = "aut"),
               person(given = "Claire",
                      family = "Ramus",
                      role = "aut"),
               person(given = "Christophe",
                      family = "Bruley",
                      role = "aut"),
               person(given = "Yohann",
                      family = "Couté",
                      role = "aut"),
               person(given = "Thomas",
                      family = "Burger",
                      role = "aut"))
as necessary.
Package required but not available: ‘MESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Alessandro Bellino <alessandro_bellino@gmx.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Arunabha Majumdar <statgen.arunabha@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Arunabha",
                      family = "Majumdar",
                      role = c("aut", "cre"),
                      email = "statgen.arunabha@gmail.com"),
               person(given = "Tanushree",
                      family = "Haldar",
                      role = "aut",
                      email = "tanushree.haldar@gmail.com"),
               person(given = "John",
                      family = "Witte",
                      role = "ctb"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yongwen Zhuang <zyongwen@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yongwen",
                    family = "Zhuang",
                    role = c("aut", "cre"),
                    email = "zyongwen@umich.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘R Barfield <barfieldrichard8@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(family = "Barfield",
                      role = "aut"),
               person(family = "R.",
                      role = "aut"),
               person(family = "Conneely",
                      role = "aut"),
               person(family = "K.",
                      role = "aut"),
               person(family = "Kilaru,V",
                      role = "aut"),
               person(given = "R",
                      family = "Barfield",
                      role = "cre",
                      email = "barfieldrichard8@gmail.com"))
as necessary.
Maintainer: ‘Jun Chen <chen.jun2@mayo.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jun",
                    family = "Chen",
                    role = c("aut", "cre"),
                    email = "Chen.Jun2@mayo.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rms', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jeremie Riou <jeremie.riou@univ-angers.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jeremie",
                      family = "Riou",
                      role = c("aut", "cre"),
                      email = "jeremie.riou@univ-angers.fr"),
               person(given = "Benoit",
                      family = "Liquet",
                      role = "aut"))
as necessary.
Maintainer: ‘Gordon J. Ross <gordon@gordonjross.co.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Gordon", "J."),
                    family = "Ross",
                    role = c("aut", "cre"),
                    email = "gordon@gordonjross.co.uk")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘crops’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
File ‘cpp11qpdf/libs/cpp11qpdf.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘libqpdf/libstatqpdf.a’
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘libqpdf/libstatqpdf.a’
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
    Object: ‘libqpdf/libstatqpdf.a’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Object: ‘libqpdf/libstatqpdf.a’
  Found ‘srandom’, possibly from ‘srandom’ (C)
    Object: ‘libqpdf/libstatqpdf.a’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘libqpdf/libstatqpdf.a’

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 nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running examples in ‘cpp4r-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pkg_template
> ### Title: Start a new project with the cpp4r package template
> ### Aliases: pkg_template
> 
> ### ** Examples
> 
> # create a new directory
> dir <- tempdir()
> dir.create(dir)
Warning in dir.create(dir) : '/tmp/RtmpByBOdp' already exists
> 
> # copy the package template into the directory
> pkg_template(dir, "mynewpkg")
Error: You must install the roxygen2 package to use this function
Execution halted
Packages required but not available: 'htmlwidgets', 'rmarkdown'

Packages suggested but not available for checking: 'shinybusy', 'shinyjqui'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Luiz O. Gavião <luiz.gaviao67@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Luiz", "O."),
                      family = "Gavião",
                      role = c("aut", "cre"),
                      email = "luiz.gaviao67@gmail.com"),
               person(given = c("Annibal", "P."),
                      family = "Sant'Anna",
                      role = "aut"),
               person(given = c("Gilson", "B.A."),
                      family = "Lima",
                      role = "aut"),
               person(given = c("Pauli", "A.A."),
                      family = "Garcia.",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rlist', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Andreas Kuehnapfel <andreas.kuehnapfel@imise.uni-leipzig.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andreas",
                    family = "Kuehnapfel",
                    role = c("aut", "cre"),
                    email = "andreas.kuehnapfel@imise.uni-leipzig.de")
as necessary.
Maintainer: ‘Ning Yilin <ningyilinnyl@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ning",
                      family = "Yilin",
                      role = c("aut", "cre"),
                      email = "ningyilinnyl@gmail.com"),
               person(given = c("Tan", "Chuen"),
                      family = "Seng",
                      role = "aut"))
as necessary.
Package required but not available: ‘rgl’

Packages suggested but not available for checking: 'knitr', 'qwraps2'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jacob Anhøj <jacob@anhoej.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jacob",
                      family = "Anhoej",
                      role = "aut"),
               person(given = "Jacob",
                      family = "Anhøj",
                      role = "cre",
                      email = "jacob@anhoej.net"))
as necessary.
Maintainer: ‘Taylor Brown <trb5me@virginia.edu>’

The Description field contains
  Doucet and Pitt (2017) <arXiv:1511.04992>. If the 'rho=' argument of
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Specified C++11: support will be removed soon
Maintainer: ‘Stefanie Krügel <stefanie.kruegel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Stefanie",
                      family = "Krügel",
                      role = c("aut", "cre"),
                      email = "stefanie.kruegel@gmail.com"),
               person(given = c("Alessandra", "R."),
                      family = "Brazzale"),
               person(role = "aut"),
               person(given = "Helmut",
                      family = "Kuechenhoff",
                      role = "aut"))
as necessary.
Packages required but not available: 'Hmisc', 'knitr'

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Johann Gagnon-Bartsch <johanngb@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Johann",
                    family = "Gagnon-Bartsch",
                    role = c("aut", "cre"),
                    email = "johanngb@umich.edu")
as necessary.
Maintainer: ‘Jueyu Gao <jueyu@ualberta.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jueyu", "Gao", "&", "Linglong"),
                      family = "Kong",
                      role = "aut"),
               person(given = "Jueyu",
                      family = "Gao",
                      role = "cre",
                      email = "jueyu@ualberta.ca"))
as necessary.
Maintainer: ‘Francesco Bartolucci <francesco.bartolucci@unipg.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Francesco",
                      family = "Bartolucci",
                      role = c("aut", "cre"),
                      email = "francesco.bartolucci@unipg.it",
                      comment = "University of Perugia"),
               person(given = "Claudia",
                      family = "Pigini",
                      role = "aut",
                      comment = "University of Ancona \"Politecnica delle Marche\""),
               person(given = "Francesco",
                      family = "Valentini",
                      role = "aut",
                      comment = "University of Ancona \"Politecnica delle Marche\""))
as necessary.
Maintainer: ‘Francis Huang <flhuang2000@yahoo.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) sharedat.Rd:23: Lost braces
    23 | \doi{10.7910/DVN/YXMQZM}{Harvard dataverse}
       |                         ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Carsten Franz <carsten.franz@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Carsten",
                    family = "Franz",
                    role = c("aut", "cre"),
                    email = "carsten.franz@gmail.com")
as necessary.
Packages required but not available: 'DT', 'keras'

Packages suggested but not available for checking:
  'covr', 'kableExtra', 'profvis', 'devtools', 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'visNetwork', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'gtsummary', 'flextable', 'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jim Lemon <drjimlemon@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jim",
                      family = "Lemon,",
                      role = "aut",
                      email = "drjimlemon@gmail.com"),
               person(given = "Jim",
                      family = "Lemon",
                      role = "cre",
                      email = "drjimlemon@gmail.com"))
as necessary.
Maintainer: ‘Gábor Csárdi <csardi.gabor@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gábor",
                    family = "Csárdi",
                    role = c("aut", "cre"),
                    email = "csardi.gabor@gmail.com")
as necessary.
Package required but not available: ‘visNetwork’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Nick Kunz <nick.kunz@columbia.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nick",
                    family = "Kunz",
                    role = c("aut", "cre"),
                    email = "nick.kunz@columbia.edu")
as necessary.
Maintainer: ‘Devin S. Johnson <devin.johnson@noaa.gov>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) crwPredict.Rd:54-68: Lost braces
    54 | \item("predTime"){
       |                  ^
checkRd: (-1) crwPredict.Rd:59: Lost braces
    59 |  no longer the default (see \item{return.type}). If the original data were 
       |                                  ^
Package required but not available: ‘scoringRules’

Packages suggested but not available for checking:
  'knitr', 'memisc', 'quarto'

VignetteBuilder package required for checking but not installed: ‘quarto’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
No news entries found.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Patrick Schnell <schnell.31@osu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Patrick",
                      family = "Schnell",
                      role = c("aut", "cre"),
                      email = "schnell.31@osu.edu"),
               person(given = "Brad",
                      family = "Carlin",
                      role = "aut"))
as necessary.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘SuperLearner’

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tinniam V Ganesh <tvganesh.85@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Tinniam", "V"),
                    family = "Ganesh",
                    role = c("aut", "cre"),
                    email = "tvganesh.85@gmail.com")
as necessary.
Maintainer: ‘Jason D. Nielsen <jdn@math.carleton.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Jason", "D."),
                    family = "Nielsen",
                    role = c("aut", "cre"),
                    email = "drjdnielsen@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘gt’

Packages suggested but not available for checking: 'spelling', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ashley Petersen <ashleyjpete@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ashley",
                    family = "Petersen",
                    role = c("aut", "cre"),
                    email = "ashleyjpete@gmail.com")
as necessary.
Packages required but not available: 'rtracklayer', 'DT'

Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Rubens Jose Rosa <rubens@rubensjoserosa.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'DiagrammeR', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘DiagrammeR’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'ggpmisc', 'sccore'

Packages suggested but not available for checking:
  'conos', 'pagoda2', 'Seurat', 'SoupX'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Henning Redestig <henning.red@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Henning",
                    family = "Redestig",
                    role = c("aut", "cre"),
                    email = "henning.red@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) normFit.Rd:39: Lost braces; missing escapes or markup?
    39 | {analytes}}
       | ^
checkRd: (-1) normPred.Rd:27: Lost braces
    27 | ode{standards}, \code{analytes}}
       |    ^
Packages required but not available: 'kableExtra', 'knitr'

Packages suggested but not available for checking:
  'bookdown', 'covr', 'DiagrammeR', 'quarto', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'quarto'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Xiaowei Zhan <zhanxw@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Xiaowei",
                    family = "Zhan",
                    role = c("aut", "cre"),
                    email = "zhanxw@gmail.com")
as necessary.
Package required but not available: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/tutorial01.Rnw’
   ‘inst/doc/tutorial02.Rnw’
   ‘inst/doc/tutorial03.Rnw’
   ‘inst/doc/tutorial04.Rnw’
   ‘inst/doc/tutorial05.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Mohamed", "El", "Fodil"),
                    family = "Ihaddaden",
                    role = c("aut", "cre"),
                    email = "ihaddaden.fodeil@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'lidR', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘crop.R’ ‘helpers.R’
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Bjoern Bornkamp <bbnkmp@mail.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Martin", "Oliver"),
                      family = "Sailer",
                      role = "aut"),
               person(given = "Bjoern",
                      family = "Bornkamp",
                      role = "cre",
                      email = "bbnkmp@mail.de"))
as necessary.
Package required but not available: ‘rms’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kornelius Rohmeyer <rohmeyer@small-projects.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kornelius",
                    family = "Rohmeyer",
                    role = c("aut", "cre"),
                    email = "rohmeyer@small-projects.de")
as necessary.
Packages required but not available: 'rJava', 'JavaGD'

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/Crossover.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘flextable’

Packages suggested but not available for checking:
  'covr', 'gt', 'expss', 'Hmisc', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Pein Florian <f.pein@lancaster.ac.uk>’

The Description field contains
  <arXiv:2112.03220>. Can be customised by providing different
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Korbinian Strimmer <strimmerlab@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Korbinian",
                      family = "Strimmer.",
                      role = "aut"),
               person(given = "Korbinian",
                      family = "Strimmer",
                      role = "cre",
                      email = "strimmerlab@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Javier Espinosa <javier.espinosa.b@usach.cl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Javier",
                    family = "Espinosa",
                    role = c("aut", "cre"),
                    email = "javier.espinosa.b@usach.cl")
as necessary.
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                                                                                    ^
checkRd: (-1) confRegCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                                                                                      ^
checkRd: (-1) confRegUCRandUCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Aurelien Latouche <aurelien.latouche@cnam.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bingqing",
                      family = "Zhou",
                      role = "aut"),
               person(given = "Aurelien",
                      family = "Latouche",
                      role = c("aut", "cre"),
                      email = "aurelien.latouche@cnam.fr"))
as necessary.
Maintainer: ‘Michael Klein <michael.klein@yale.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Klein",
                    role = c("aut", "cre"),
                    email = "michael.klein@yale.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
'library' or 'require' call not declared from: ‘ggplot2’
Package required but not available: ‘mapview’

Package suggested but not available for checking: ‘mapboxapi’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dae Woong Ham <daewoongham@g.harvard.edu>’

The Description field contains
  to Test Causal Hypotheses in Conjoint Analysis" <arXiv:2201.08343>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael A Rotondi <mrotondi@yorku.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Michael", "A"),
                    family = "Rotondi",
                    role = c("aut", "cre"),
                    email = "mrotondi@yorku.ca")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'INLA'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘lmtp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'lintr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [99s/110s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(
  +     vignettes = TRUE, error = identical(Sys.getenv("GITHUB_ACTION"), "true")
  + )
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Benjamin M. Taylor <benjamin.taylor.software@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Benjamin", "M.", "Taylor", "Additional", "contributions", "Bikash", "Parida", "Jacob"),
                      family = "Davies",
                      role = "aut"),
               person(given = c("Benjamin", "M."),
                      family = "Taylor",
                      role = "cre",
                      email = "benjamin.taylor.software@gmail.com"))
as necessary.
checkRd: (-1) cruts-package.Rd:21: Lost braces
    21 | section{Dependencies}{
       |        ^
checkRd: (-1) cruts-package.Rd:21-24: Lost braces
    21 | section{Dependencies}{
       |                      ^
checkRd: (-1) cruts-package.Rd:26: Lost braces
    26 | section{Citation}{
       |        ^
checkRd: (-1) cruts-package.Rd:26-28: Lost braces
    26 | section{Citation}{
       |                  ^
checkRd: (-1) cruts-package.Rd:30-32: Lost braces
    30 | references{
       |           ^
Maintainer: ‘Ziqiang Lin <ziqiang.lin@nyulangone.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ziqiang",
                      family = "Lin",
                      role = c("aut", "cre"),
                      email = "ziqiang.lin@nyulangone.org"),
               person(given = c("Eugene", "M"),
                      family = "Laska",
                      role = "aut"),
               person(given = c("Carole", "E"),
                      family = "Siegel",
                      role = "aut"),
               person(given = "Wangjian",
                      family = "Zhang",
                      role = "aut"),
               person(given = "Qiaoxuan",
                      family = "Lin",
                      role = "aut"),
               person(given = "Bo",
                      family = "Ye.",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Vivian R. Steiger <viv.datascientist@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Vivian", "R."),
                    family = "Steiger",
                    role = c("aut", "cre"),
                    email = "viv.datascientist@gmail.com")
as necessary.
Maintainer: ‘Haydar Demirhan <haydar.demirhan@rmit.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Haydar",
                    family = "Demirhan",
                    role = c("aut", "cre"),
                    email = "haydar.demirhan@rmit.edu.au",
                    comment = c(ORCID = "0000-0002-8565-4710"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Claudio Pozo Valenzuela <claudiopozova@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Claudio", "Pozo"),
                      family = "Valenzuela",
                      role = c("aut", "cre"),
                      email = "claudiopozova@gmail.com"),
               person(given = "Saddys",
                      family = "Rodriguez-Llamazares",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'plnr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Zhicheng Du<dgdzc@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhicheng",
                      family = "Du",
                      role = c("aut", "cre"),
                      email = "dgdzc@hotmail.com"),
               person(given = "Yuantao",
                      family = "Hao",
                      role = "aut"))
as necessary.
Packages required but not available: 'rms', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Michael P. Fay <mfay@niaid.nih.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sungwook",
                      family = "Kim",
                      role = "aut"),
               person(given = c("Michael", "P."),
                      family = "Fay",
                      role = "cre",
                      email = "mfay@niaid.nih.gov"))
as necessary.
Maintainer: ‘Peter Wu <peter123wu0@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Peter",
                    family = "Wu",
                    role = c("aut", "cre"),
                    email = "peter123wu0@gmail.com")
as necessary.
Packages required but not available: 'tidyverse', 'riskRegression'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'gt', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'DiagrammeR', 'knitr', 'prettydoc', 'plotly', 'rmarkdown',
  'listviewer', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Anantha Janakiraman <anantharaman.j@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Anantha",
                    family = "Janakiraman",
                    role = c("aut", "cre"),
                    email = "anantharaman.j@gmail.com")
as necessary.
Packages required but not available: 'smarter', 'GenomicFeatures'

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'leaflet'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Koen W. De Bock <kdebock@audencia.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Koen", "W."),
                      family = "De Bock",
                      role = c("aut", "cre"),
                      email = "kdebock@audencia.com"),
               person(given = "Kristof",
                      family = "Coussement",
                      role = "aut"),
               person(given = "Stefan",
                      family = "Lessmann",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Aixiang Jiang <aijiang@bccrc.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Aixiang",
                    family = "Jiang",
                    role = c("aut", "cre", "cph"),
                    email = "aijiang@bccrc.ca",
                    comment = c(ORCID = "0000-0002-6153-7595"))
as necessary.

The Description field contains
  <arXiv:1603.02754>, - Aoki et al. (2023) <doi:10.1200/JCO.23.01115>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available: 'Hmisc', 'rms', 'survminer'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dmitry Pavlyuk <Dmitry.V.Pavlyuk@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dmitry",
                      family = "Pavlyuk",
                      role = c("aut", "cre"),
                      email = "dmitry.v.pavlyuk@gmail.com"),
               person(given = "Eugene",
                      family = "Girtcius",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'leaflet'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Junho Yang <junhoyang@stat.tamu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Junho",
                    family = "Yang",
                    role = c("aut", "cre"),
                    email = "junhoyang@stat.tamu.edu")
as necessary.
Maintainer: ‘Caleb Lucas <calebjlucas@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Caleb",
                      family = "Lucas",
                      role = c("aut", "cre"),
                      email = "calebjlucas@gmail.com",
                      comment = "https://caleblucas.com/"),
               person(given = "Joshua",
                      family = "McCrain",
                      role = "aut",
                      comment = "http://joshuamccrain.com/"))
as necessary.
Maintainer: ‘Caleb Lucas <calebjlucas@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Caleb",
                      family = "Lucas",
                      role = c("aut", "cre"),
                      email = "calebjlucas@gmail.com",
                      comment = "https://caleblucas.com/"),
               person(given = "Joshua",
                      family = "McCrain",
                      role = "aut",
                      comment = "http://joshuamccrain.com/"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'lidR', 'rgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'DiagrammeR', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Deniz Yenigun <deniz.yenigun@bilgi.edu.tr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Deniz",
                      family = "Yenigun",
                      role = c("aut", "cre"),
                      email = "deniz.yenigun@bilgi.edu.tr"),
               person(given = "Gunes",
                      family = "Ertan",
                      role = "aut"),
               person(given = "Michael",
                      family = "Siciliano",
                      role = "aut"))
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘atm.Rd’:
    http://dx.doi.org/10.1016/j.socnet.2012.06.004
  File ‘cssTools-package.Rd’:
    http://dx.doi.org/10.1016/0378-8733(87)90009-8
  File ‘highTechManagers.Rd’:
    http://dx.doi.org/10.1016/0378-8733(87)90009-8
  File ‘s14.Rd’:
    http://dx.doi.org/10.1007/BF01896809
  File ‘sliceQuality.Rd’:
    http://dx.doi.org/10.1016/0378-8733(87)90009-8
    http://dx.doi.org/10.1016/j.socnet.2012.06.004
Maintainer: ‘Jonas M. B. Haslbeck <jonas.haslbeck@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jonas", "M.", "B."),
                      family = "Haslbeck",
                      role = c("aut", "cre"),
                      email = "jonas.haslbeck@gmail.com"),
               person(given = c("Dirk", "U."),
                      family = "Wulff",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gt'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tim Bergsma <bergsmat@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tim",
                    family = "Bergsma",
                    role = c("aut", "cre"),
                    email = "bergsmat@gmail.com")
as necessary.
Maintainer: ‘Robin Gower <csvwr@infonomics.ltd.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Robin",
                    family = "Gower",
                    role = c("aut", "cre"),
                    email = "csvwr@infonomics.ltd.uk")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Thomas J. Leeper <thosjleeper@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘yaml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kartikeya",
                    family = "Bolar",
                    role = c("aut", "cre"),
                    email = "kartikeya.bolar@tapmi.edu.in")
as necessary.
Package required but not available: ‘rpivotTable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Francois Ritter <ritter.francois@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Clark Fitzgerald <fitzgerald@csus.edu>’

The BugReports field in DESCRIPTION has
  https://github.com/julianofhernandez/ctf
which should likely be
  https://github.com/julianofhernandez/ctf/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ningning Xu <ningningxu312@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ningning",
                    family = "Xu",
                    role = c("aut", "cre"),
                    email = "ningningxu312@gmail.com")
as necessary.
Maintainer: ‘Danny Arends <Danny.Arends@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Danny",
                      family = "Arends",
                      role = c("aut", "cre"),
                      email = "Danny.Arends@gmail.com"),
               person(given = "Yang",
                      family = "Li",
                      role = "aut"),
               person(given = c("Gudrun", "A"),
                      family = "Brockmann",
                      role = "aut"),
               person(given = c("Ritsert", "C"),
                      family = "Jansen",
                      role = "aut"),
               person(given = c("Robert", "W"),
                      family = "Williams",
                      role = "aut"),
               person(given = "Pjotr",
                      family = "Prins",
                      role = "aut"))
as necessary.
Package required but not available: ‘qtl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Cheng Ju <jucheng1992@gmail.com>’

The Description field contains
  algorithm (Ju et al. (2017) <arXiv:1706.10029>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available: 'SuperLearner', 'tmle'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

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

Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/ctsemOMX.rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'knitr', 'devtools', 'papaja'

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/hierarchicalmanual.rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kartikeya",
                    family = "Bolar",
                    role = c("aut", "cre"),
                    email = "kartikeya.bolar@tapmi.edu.in")
as necessary.
Packages required but not available: 'rmarkdown', 'rhandsontable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kartikeya",
                    family = "Bolar",
                    role = c("aut", "cre"),
                    email = "kartikeya.bolar@tapmi.edu.in")
as necessary.
Packages required but not available: 'rmarkdown', 'rhandsontable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘John T. Willse <jtwillse@uncg.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("John", "T."),
                    family = "Willse",
                    role = c("aut", "cre"),
                    email = "jtwillse@uncg.edu")
as necessary.
Maintainer: ‘John T. Willse <willse@uncg.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("John", "T."),
                    family = "Willse",
                    role = c("aut", "cre"),
                    email = "willse@uncg.edu")
as necessary.
Found the following files/directories:
  ‘Hello.csv’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'countcolors', 'devtools', 'DT', 'htmlTable', 'kableExtra', 'knitr',
  'prettydoc', 'rmarkdown', 'rmdformats'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘apply_by_blocks.R’ ‘balance_by_blocks.Rd’ ‘balance_matrix.R’
    ‘balance_matrix.Rd’ ‘make_non_negative.Rd’ ‘round_by_blocks.Rd’
    ‘round_matrix.R’ ‘round_matrix.Rd’ ‘round_vector.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'rmarkdown', 'knitr', 'leaflet', 'plotly'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘accessors.Rd’ ‘as-cubble.R’ ‘as_cubble.Rd’ ‘check-key.R’
    ‘climate-data.Rd’ ‘covid.Rd’ ‘cubble-attrs.R’ ‘cubble-class.R’
    ‘cubble-print.R’ ‘dplyr.R’ ‘dplyr.Rd’ ‘face-spatial-temporal.R’
    ‘face.Rd’ ‘glyph.R’ ‘glyph.Rd’ ‘make_spatial_sf.Rd’
    ‘make_temporal_tsibble.Rd’ ‘matching.R’ ‘matching.Rd’ ‘netcdf.R’
    ‘sf.R’ ‘test-data.Rd’ ‘tsibble.R’ ‘tsibble.Rd’ ‘unfold.R’ ‘unfold.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Wei-Chen Chen <wccsnow@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Alec Stephenson <alec_stephenson@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alec",
                      family = "Stephenson.",
                      role = "aut"),
               person(given = "Alec",
                      family = "Stephenson",
                      role = "cre",
                      email = "alec_stephenson@hotmail.com"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Description field contains
  solvers. See Rokicki, T. (2008) <arXiv:0803.3435> for the Kociemba
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/CUBvignette-knitr.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'shinytest2', 'covr', 'knitr', 'rmarkdown', 'quarto', 'pkgdown'

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Charles-Édouard Giguère <ce.giguere@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Charles-Édouard",
                    family = "Giguère",
                    role = c("aut", "cre"),
                    email = "ce.giguere@gmail.com")
as necessary.
Package required but not available: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kevin Stadler <a00425926@unet.univie.ac.at>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘mantel.test.Rd’:
    https://doi.org/10.1093/sysbio/32.1.21
    https://doi.org/10.1086/341527
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Shuo Li <skyli@bu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Shuo",
                      family = "Li",
                      role = c("aut", "cre"),
                      email = "skyli@bu.edu"),
               person(given = "Xuan",
                      family = "Liu",
                      role = "aut",
                      email = "liuxuan@bu.edu"),
               person(given = "Qiong",
                      family = "Yang",
                      role = "aut",
                      email = "qyang@bu.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘create_cure_dataframe.R’ ‘cure_plot.R’ ‘resample_residuals.R’
Package required but not available: ‘relsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...5a6
> All Done!
  Running ‘testthat.R’ [8s/74s]
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Eva Koritakova <koritakova@iba.muni.cz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Eva",
                      family = "Koritakova",
                      role = c("aut", "cre"),
                      email = "koritakova@iba.muni.cz",
                      comment = c(ROR = "Janousova")),
               person(given = "Tomas",
                      family = "Pavlik",
                      role = "aut"),
               person(given = "Jiri",
                      family = "Mayer",
                      role = "aut"),
               person(given = "Ladislav",
                      family = "Dusek",
                      role = "aut"))
as necessary.
Package required but not available: ‘visNetwork’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Maintainer: ‘Thomas Lin Pedersen <thomasp85@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Thomas", "Lin"),
                    family = "Pedersen",
                    role = c("aut", "cre"),
                    email = "thomasp85@gmail.com")
as necessary.
Maintainer: ‘Chris Mann <cmann3@unl.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chris",
                    family = "Mann",
                    role = c("aut", "cre"),
                    email = "cmann3@unl.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Christopher Murphy <cmurphy0313@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kimihiro",
                      family = "Noguchi",
                      role = "aut",
                      email = "kimihiro.noguchi@wwu.edu"),
               person(given = "Christopher",
                      family = "Murphy",
                      role = "cre",
                      email = "cmurphy0313@gmail.com"))
as necessary.
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Koen W. De Bock <kdebock@audencia.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Koen", "W."),
                    family = "De Bock",
                    role = c("aut", "cre"),
                    email = "kdebock@audencia.com")
as necessary.
Maintainer: ‘Paul Kabaila <p.kabaila@latrobe.edu.au>’

The Description field contains
  Kabaila (2022) <arXiv:2211.04729>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available: 'rmarkdown', 'knitr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Iago Montero Nunez <iagomontero95@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Iago", "Montero"),
                      family = "Nuñez",
                      role = "aut"),
               person(given = c("Iago", "Montero"),
                      family = "Nunez",
                      role = "cre",
                      email = "iagomontero95@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Boxiang Wang <boxiang-wang@uiowa.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Douglas", "M."),
                      family = "Hawkins",
                      role = "aut"),
               person(given = c("David", "H."),
                      family = "Olwell",
                      role = "aut"),
               person(given = "Boxiang",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "boxiang-wang@uiowa.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

Package which this enhances but not available for checking: ‘covr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'set', 'do'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yimin Chen <chenyimin0226@126.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yimin",
                      family = "Chen",
                      role = c("aut", "cre"),
                      email = "chenyimin0226@126.com"),
               person(given = "Zhang",
                      family = "Jinxin",
                      role = "aut"))
as necessary.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cvar)
  > 
  > test_check("cvar")
  Failed with error:  'there is no package called 'fGarch''
  Saving _problems/test-garch-54.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-garch.R:54:5'): garch1c1 related functions work ok ─────────────
  Error in `.get_dist_elem("std", "r")`: requested distribution property needs package fGarch
  please install package 'fGarch' and try again
  Backtrace:
      ▆
   1. └─cvar:::.get_dist_elem("std", "r") at test-garch.R:54:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ]
  Error:
  ! Test failures.
  Execution halted
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxyglobals'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Erin LeDell <oss@ledell.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Erin",
                      family = "LeDell",
                      role = c("aut", "cre"),
                      email = "oss@ledell.org"),
               person(given = "Maya",
                      family = "Petersen",
                      role = "aut"),
               person(given = "Mark",
                      family = "van der Laan",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'gt', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jose Gama <rxprtgama@gmail.com>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘scoreRoth28Graphic.Rd’:
    http://dx.doi.org/10.1016/S0042-6989(97)00433-1
Maintainer: ‘Ben Marwick <benmarwick@gmail.com>’

Found the following (possibly) invalid file URIs:
  URI: www.jstor.org/stable/90707
    From: inst/doc/how_to_test_CVs.html
  URI: CONDUCT.md
    From: README.md
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pkgdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Romain Azais <romain.azais@inria.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Romain",
                      family = "Azais",
                      role = c("aut", "cre"),
                      email = "romain.azais@inria.fr"),
               person(given = "Sandie",
                      family = "Ferrigno",
                      role = "aut"),
               person(given = "Marie-Jose",
                      family = "Martinez",
                      role = "aut"))
as necessary.
Package required but not available: ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'ggimage', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tammo Krueger <tammokrueger@googlemail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tammo",
                      family = "Krueger",
                      role = c("aut", "cre"),
                      email = "tammokrueger@googlemail.com"),
               person(given = "Mikio",
                      family = "Braun",
                      role = "aut"))
as necessary.
Maintainer: ‘Donghoh Kim <donghoh.kim@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Donghoh",
                      family = "Kim",
                      role = c("aut", "cre"),
                      email = "donghoh.kim@gmail.com"),
               person(given = "Hee-Seok",
                      family = "Oh",
                      role = "aut",
                      email = "heeseok@stats.snu.ac.kr"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

Packages which this enhances but not available for checking:
  'gurobi', 'rcbc'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jiqiang Guo <guojq28@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jiqiang",
                    family = "Guo",
                    role = c("aut", "cre"),
                    email = "guojq28@gmail.com")
as necessary.
Maintainer: ‘Gabor Csardi <csardi.gabor@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gabor",
                    family = "Csardi",
                    role = c("aut", "cre"),
                    email = "csardi.gabor@gmail.com")
as necessary.
Maintainer: ‘Peter Biber <castor.fiber@gmx.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Peter",
                    family = "Biber",
                    role = c("aut", "cre"),
                    email = "castor.fiber@gmx.de")
as necessary.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'BiocStyle'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'rmarkdown', 'knitr'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘mixOmics’

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Seurat'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Christopher Gandrud <christopher.gandrud@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christopher",
                    family = "Gandrud",
                    role = c("aut", "cre"),
                    email = "christopher.gandrud@gmail.com")
as necessary.
Package required but not available: ‘htmlwidgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mauricio Vargas <oec@media.mit.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mauricio",
                      family = "Vargas",
                      role = c("aut", "cre"),
                      email = "oec@media.mit.edu"),
               person(given = "Joshua",
                      family = "Kunst",
                      role = "aut"),
               person(given = "Dave",
                      family = "Landry",
                      role = "ctb"),
               person(family = "Datawheel",
                      role = "cph"))
as necessary.
Package required but not available: ‘htmlwidgets’

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

Packages suggested but not available for checking:
  'knitr', 'golem', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

Packages suggested but not available for checking:
  'knitr', 'roxygen2', 'XLConnect', 'xlsx'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘John Maindonald <jhmaindonald@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "John",
                    family = "Maindonald",
                    role = c("aut", "cre"),
                    email = "jhmaindonald@gmail.com")
as necessary.
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/marray-notes.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'kableExtra', 'knitr'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘yaml’

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘James Curran <j.curran@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "James",
                      family = "Curran",
                      role = c("aut", "cre"),
                      email = "j.curran@auckland.ac.nz"),
               person(given = "Danny",
                      family = "Chang",
                      role = "aut"))
as necessary.
checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
Maintainer: ‘Graham Goff <goffgrahamc@gmail.com>’

Found the following (possibly) invalid URLs:
  URL: %22https://grahamgoff.github.io/DAGassist/articles/ecosystem.html%22
    From: README.md
    Message: Invalid URI scheme
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'modelsummary', 'rmarkdown', 'tidyverse',
  'DiagrammeR'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Johannes Textor <johannes.textor@gmx.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Johannes",
                      family = "Textor",
                      role = c("aut", "cre"),
                      email = "johannes.textor@gmx.de"),
               person(given = "Benito",
                      family = "van der Zander",
                      role = "aut"),
               person(given = "Ankur",
                      family = "Ankan",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Lutz P Breitling <l.breitling@posteo.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Lutz", "P"),
                    family = "Breitling",
                    role = c("aut", "cre"),
                    email = "l.breitling@posteo.de")
as necessary.
Maintainer: ‘Niklas Hohmann <Niklas.Hohmann@fau.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Niklas",
                    family = "Hohmann",
                    role = c("aut", "cre"),
                    email = "niklas.hohmann@fau.de")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rmarkdown', 'reactable'

Packages suggested but not available for checking:
  'covr', 'knitr', 'diffviewer'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'ggimage'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'ggtree', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ali Uenlue <ali.uenlue@tum.de>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Szymon Maksymiuk <sz.maksymiuk@gmail.com>’

The Description field contains
  'DALEXtra' creates 'DALEX' Biecek (2018) <arXiv:1806.08915> explainer
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Running examples in ‘DALEXtra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: explain_xgboost
> ### Title: Create explainer from your xgboost model
> ### Aliases: explain_xgboost
> 
> ### ** Examples
> 
> library("xgboost")
> library("DALEXtra")
> library("mlr")
Loading required package: ParamHelpers
> # 8th column is target that has to be omitted in X data
> data <- as.matrix(createDummyFeatures(titanic_imputed[,-8]))
> model <- xgboost(data, titanic_imputed$survived, nrounds = 10,
+                  params = list(objective = "binary:logistic"),
+                 prediction = TRUE)
Warning in throw_err_or_depr_msg("Parameter(s) have been removed from this function: ",  :
  Parameter(s) have been removed from this function: params. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: prediction. This warning will become an error in a future version.
> # explainer with encode functiom
> explainer_1 <- explain_xgboost(model, data = titanic_imputed[,-8],
+                                titanic_imputed$survived,
+                                encode_function = function(data) {
+  as.matrix(createDummyFeatures(data))
+ })
Preparation of a new explainer is initiated
  -> model label       :  xgb.Booster  ( [33m default [39m )
  -> data              :  2207  rows  7  cols 
  -> target variable   :  2207  values 
  -> predict function  :  yhat.xgb.Booster  will be used ( [33m default [39m )
  -> predicted values  :  No value for predict function target column. ( [33m default [39m )
Error in strsplit(model$params$objective, ":", fixed = TRUE) : 
  non-character argument
Calls: explain_xgboost ... explain -> model_info -> model_info.xgb.Booster -> strsplit
Execution halted
Package required but not available: ‘FSelector’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Brecht Devleesschauwer <brechtdv@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘DALY-package.Rd’:
    http://dx.doi.org/10.1007/s00038-014-0552-z
  File ‘DALYcalculator.Rd’:
    http://dx.doi.org/10.1007/s00038-014-0552-z
  File ‘setStdLE.Rd’:
    http://dx.doi.org/10.1007/s00038-014-0552-z
Cannot process vignettes
Packages suggested but not available for checking:
  'Seurat', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘leaflet’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Damian Siniakowicz <DamianSiniakowicz@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Damian",
                    family = "Siniakowicz",
                    role = c("aut", "cre"),
                    email = "damiansiniakowicz@gmail.com")
as necessary.
Maintainer: ‘Rampal S. Etienne <r.s.etienne@rug.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Rampal", "S.", "Etienne", "&", "Alex", "L."),
                      family = "Pigot",
                      role = "aut"),
               person(given = c("Rampal", "S."),
                      family = "Etienne",
                      role = "cre",
                      email = "r.s.etienne@rug.nl"))
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David Garibay <dgari039@uottawa.ca>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘beta_params.Rd’:
    \keyword{distribution;}
  File ‘calc_evpi.Rd’:
    \keyword{information;}
  File ‘dirichlet_params.Rd’:
    \keyword{distribution;}
  File ‘gamma_params.Rd’:
    \keyword{distribution;}
  File ‘lnorm_params.Rd’:
    \keyword{distribution;}
Cannot process vignettes
Packages suggested but not available for checking:
  'lintr', 'knitr', 'rmarkdown', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Dirk Eddelbuettel <edd@debian.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Dirk", "Eddelbuettel", "with", "contributions", "by", "Brodie"),
                      family = "Gaslam",
                      role = "aut"),
               person(given = "Kevin",
                      family = "Denny",
                      role = "aut"),
               person(given = "Kabira",
                      family = "Namit",
                      role = "aut"),
               person(given = "Colin",
                      family = "Gillespie",
                      role = "aut"),
               person(given = "R",
                      family = "Core",
                      role = "aut"),
               person(given = "Josh",
                      family = "Ulrich",
                      role = "aut"),
               person(given = c("Jordan", "Mark"),
                      family = "Barbone",
                      role = "aut"),
               person(given = "Bill",
                      family = "Dunlap",
                      role = "aut"),
               person(family = "others.",
                      role = "aut"),
               person(given = "Dirk",
                      family = "Eddelbuettel",
                      role = "cre",
                      email = "edd@debian.org"))
as necessary.
Maintainer: ‘Matteo Quartagno <m.quartagno@ucl.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Matteo",
                    family = "Quartagno",
                    role = c("aut", "cre"),
                    email = "m.quartagno@ucl.ac.uk")
as necessary.

The Description field contains
  et al. (2019) <arXiv:1905.00241>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Dorota Desaulle <dorota.desaulle@u-paris.fr>’

The Description field contains
  <arXiv:2103.09872>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Carlos P. Carmona <perezcarmonacarlos@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Carlos", "P."),
                      family = "Carmona",
                      role = c("aut", "cre"),
                      email = "perezcarmonacarlos@gmail.com"),
               person(given = "Meelis",
                      family = "Partel",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘SNPassoc’

Packages suggested but not available for checking:
  'devtools', 'knitr', 'leaflet', 'leaflet.minicharts', 'networkD3',
  'plotly', 'rgl', 'rmarkdown'

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

Package suggested but not available for checking: ‘spelling’

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

Package suggested but not available for checking: ‘leaflet’

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

Packages suggested but not available for checking:
  'devtools', 'knitr', 'leaflet', 'leaflet.minicharts', 'networkD3',
  'plotly', 'rgl', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

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

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

Package suggested but not available for checking: ‘PopGenReport’

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

Packages suggested but not available for checking:
  'dartR.base', 'dartR.sim', 'dartR.captive', 'dartR.popgen',
  'dartR.spatial'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'lintr', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Martijn Schuemie <schuemie@ohdsi.org>’

Found the following (possibly) invalid file URI:
  URI: ../../issues
    From: README.md
Package required but not available: ‘rJava’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rgl', 'ProjectionBasedClustering'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Xiaorui(Jeremy) Zhu <zhuxiaorui1989@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xiaorui",
                      family = "Zhu",
                      role = "aut",
                      comment = "Jeremy"),
               person(given = "Xiaorui",
                      family = "Zhu",
                      role = "cre",
                      email = "zhuxiaorui1989@gmail.com",
                      comment = "Jeremy"))
as necessary.
Package required but not available: ‘xlsx’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'arsenal', 'config', 'devtools', 'DT', 'explore', 'golem', 'skimr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'knitr', 'rmarkdown', 'roxygen2', 'spelling',
  'usethis', 'covr', 'DT'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rmarkdown', 'networkD3'

Packages suggested but not available for checking: 'covr', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jonathan M. Gilligan <jonathan.gilligan@vanderbilt.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
File ‘DataGraph/libs/DataGraph.so’:
  Found non-API call to R: ‘Rf_isFrame’
This entry point may be removed soon.

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Maintainer: ‘Srivenkatesh Gandhi <srivenkateshg@sase.ssn.edu.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Srivenkatesh",
                      family = "Gandhi",
                      role = c("aut", "cre"),
                      email = "srivenkateshg@sase.ssn.edu.in"),
               person(given = c("Kreshnaa", "Raam", "S"),
                      family = "Bethusamy",
                      role = "aut",
                      email = "kreshnaaraamsb@sase.ssn.edu.in"))
as necessary.
Packages required but not available: 'xlsx', 'rChoiceDialogs'

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

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'wordcloud2', 'DT', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dania M. Rodriguez <dmrodz@gmail.com>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘my.data.Rd’:
    http://doi.org/10.5281/zenodo.439543
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Found the following files/directories:
  ‘my new data set.rds’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘DataMetProcess-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: list_inmet
> ### Title: List of data available at INMET by year
> ### Aliases: list_inmet
> 
> ### ** Examples
> 
> 
> file.down <- tempfile()
> file.save <- tempfile()
> 
> info.inmet <-
+   DataMetProcess::list_inmet(year="2000",file.down)
trying URL 'https://portal.inmet.gov.br/uploads/dadoshistoricos/2000.zip'
Warning in utils::download.file(url = base::paste0("https://portal.inmet.gov.br/uploads/dadoshistoricos/",  :
  cannot open URL 'https://portal.inmet.gov.br/uploads/dadoshistoricos/2000.zip': HTTP status was '403 Forbidden'
Error: Error downloading data for year 2000.
Possible cause: download timeout exceeded.
Suggested solution: increase the maximum download time, e.g.:
options(timeout = 1000)

Original error message: cannot open URL 'https://portal.inmet.gov.br/uploads/dadoshistoricos/2000.zip'
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'reactable', 'toastui', 'shinybusy'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'validate'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'knitr', 'rmarkdown', 'roxygen2', 'usethis', 'yaml'

Packages suggested but not available for checking: 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Chun-Sheng Liang <liangchunsheng@lzu.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chun-Sheng",
                      family = "Liang",
                      role = c("aut", "cre"),
                      email = "liangchunsheng@lzu.edu.cn"),
               person(given = "Hao",
                      family = "Wu",
                      role = "aut"),
               person(given = "Hai-Yan",
                      family = "Li",
                      role = "aut"),
               person(given = "Qiang",
                      family = "Zhang",
                      role = "aut"),
               person(given = "Zhanqing",
                      family = "Li",
                      role = "aut"),
               person(given = "Ke-Bin",
                      family = "He",
                      role = "aut"),
               person(given = "Lanzhou",
                      family = "University",
                      role = "aut"),
               person(given = "Tsinghua",
                      family = "University",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'DT', 'flexdashboard', 'flexsiteboard', 'knitr', 'rJava',
  'rmarkdown', 'plotly', 'htmlwidgets'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘drwho_directors.Rd’ ‘drwho_episodes.Rd’ ‘drwho_writers.Rd’
    ‘torchwood_directors.Rd’ ‘torchwood_episodes.Rd’
    ‘torchwood_writers.Rd’
Package required but not available: ‘rmarkdown’

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘yaml’

Packages suggested but not available for checking:
  'knitr', 'lintr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'RSDA', 'HistDAWass'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Christoph Sax <christoph.sax@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christoph",
                    family = "Sax",
                    role = c("aut", "cre"),
                    email = "christoph.sax@gmail.com")
as necessary.

The BugReports field in DESCRIPTION has
  https://github.com/christophsax/dataseries
which should likely be
  https://github.com/christophsax/dataseries/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rdflib', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Paolo Giordani <paolo.giordani@uniroma1.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Paolo",
                      family = "Giordani",
                      role = c("aut", "cre"),
                      email = "paolo.giordani@uniroma1.it"),
               person(given = c("Maria", "Brigida"),
                      family = "Ferraro",
                      role = "aut"),
               person(given = "Francesca",
                      family = "Martella",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘DT’

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running ‘testthat.R’ [124s/160s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DataSimilarity)
  > 
  > test_check("DataSimilarity")
  Saving _problems/test-MMCM-19.R
  Using automatic sigma estimation (sigest) for RBF or laplace kernel 
  Using automatic sigma estimation (sigest) for RBF or laplace kernel 
  Saving _problems/test-Petrie-17.R
  [ FAIL 2 | WARN 0 | SKIP 9 | PASS 1989 ]
  
  ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
  • empty test (9): , , , , , , , ,
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-MMCM.R:19:5'): (code run outside of `test_that()`) ─────────────
  Error in `nbmatch(data.list, n.vec, dist.fun, dist.args)`: Package "nbpMatching" required for using method nbmatch().
  Backtrace:
      ▆
   1. └─DataSimilarity (local) testMMCM(10) at test-MMCM.R:62:1
   2.   └─DataSimilarity::MMCM(X1, X2, as.data.frame(X3), X4, X5, X6, seed = i) at test-MMCM.R:19:5
   3.     └─DataSimilarity:::nbmatch(data.list, n.vec, dist.fun, dist.args)
  ── Error ('test-Petrie.R:17:5'): (code run outside of `test_that()`) ───────────
  Error in `nbmatch(data.list, n.vec, dist.fun, dist.args)`: Package "nbpMatching" required for using method nbmatch().
  Backtrace:
      ▆
   1. └─DataSimilarity (local) testPetrie(10) at test-Petrie.R:60:1
   2.   └─DataSimilarity::Petrie(X1, as.data.frame(X2), X3, X4, X5, X6) at test-Petrie.R:17:5
   3.     └─DataSimilarity:::nbmatch(data.list, n.vec, dist.fun, dist.args)
  
  [ FAIL 2 | WARN 0 | SKIP 9 | PASS 1989 ]
  Error:
  ! Test failures.
  Execution halted
Note: skipping ‘Details.Rnw’ due to unavailable dependencies: 'knitr'
Note: skipping ‘GettingStarted.Rnw’ due to unavailable dependencies:
  'knitr'
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'EML', 'rhandsontable'

Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown', 'listviewer'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Svetlana Saarela <admin@svetlanasaarela.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Svetlana",
                      family = "Saarela",
                      role = c("aut", "cre"),
                      email = "admin@svetlanasaarela.com"),
               person(given = "Anton",
                      family = "Grafström",
                      role = "aut"))
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘datassim.Rd’:
    https://doi.org/10.20944/preprints201710.0098.v1
Cannot process vignettes
Packages suggested but not available for checking: 'yaml', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
File ‘data.table/libs/data_table.so’:
  Found non-API calls to R: ‘OBJECT’, ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_OBJECT’, ‘SET_TRUELENGTH’, ‘TRUELENGTH’
This entry point may be removed soon:
‘OBJECT’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Running ‘S4.R’ [0s/1s]
  Running ‘autoprint.R’ [0s/0s]
  Comparing ‘autoprint.Rout’ to ‘autoprint.Rout.save’ ...4,10d3
< 
< Attaching package: 'data.table'
< 
< The following object is masked from 'package:base':
< 
<     %notin%
< 
  Running ‘froll.R’ [14s/18s]
  Running ‘knitr.R’ [0s/0s]
  Comparing ‘knitr.Rout’ to ‘knitr.Rout.save’ ... OK
  Running ‘main.R’ [96s/104s]
  Running ‘nafill.R’ [1s/1s]
  Running ‘other.R’ [0s/0s]
  Running ‘programming.R’ [1s/1s]
  Running ‘types.R’ [0s/1s]
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'yaml', 'networkD3', 'htmlwidgets',
  'DiagrammeR'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Running examples in ‘data.tree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.Node
> ### Title: Plot a graph, or get a graphviz dot representation of the tree
> ### Aliases: plot.Node ToDiagrammeRGraph SetNodeStyle SetEdgeStyle
> ###   SetGraphStyle GetDefaultTooltip
> 
> ### ** Examples
> 
> data(acme)
> SetGraphStyle(acme, rankdir = "TB")
> SetEdgeStyle(acme, arrowhead = "vee", color = "blue", penwidth = 2)
> #per default, Node style attributes will be inherited:
> SetNodeStyle(acme, style = "filled,rounded", shape = "box", fillcolor = "GreenYellow", 
+              fontname = "helvetica", tooltip = GetDefaultTooltip)
> SetNodeStyle(acme$IT, fillcolor = "LightBlue", penwidth = "5px")
> #inheritance can be avoided:
> SetNodeStyle(acme$Accounting, inherit = FALSE, fillcolor = "Thistle", 
+              fontcolor = "Firebrick", tooltip = "This is the accounting department")
> SetEdgeStyle(acme$Research$`New Labs`, 
+              color = "red", 
+              label = "Focus!", 
+              penwidth = 3, 
+              fontcolor = "red")
> #use Do to set style on specific nodes:
> Do(acme$leaves, function(node) SetNodeStyle(node, shape = "egg"))
> plot(acme)
Error in plot.Node(acme) : 
  Package "DiagrammeR" is required to plot a `data.tree::Node`object. Please install it.
Calls: plot -> plot.Node
Execution halted
Running ‘testthat.R’ [9s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("data.tree")
  Loading required package: data.tree
  Saving _problems/test-draw-145.R
                            levelName    cost
  1  Acme Inc.                             NA
  2   ¦--Accounting                        NA
  3   ¦   ¦--New Software             1000000
  4   ¦   °--New Accounting Standards  500000
  5   ¦--Research                          NA
  6   ¦   ¦--New Product Line         2000000
  7   ¦   °--New Labs                  750000
  8   °--IT                                NA
  9       ¦--Outsource                 400000
  10      ¦--Go agile                  250000
  11      °--Switch to R                50000
    levelName  b             1
  1 Root      NA              
  2  °--a      2              
  3      °--c NA 1, 2, 3, 4, 5
    levelName a
  1     Root   
  2      °--a 2
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 366 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • empty test (1):
  • {DiagrammeR} is not installed (3): 'test-draw.R:30:3', 'test-draw.R:53:3',
    'test-draw.R:95:3'
  • {yaml} is not installed. (3): 'test-treeConversionList.R:201:3',
    'test-treeConversionList.R:231:3', 'test-treeConversionList.R:263:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-draw.R:144:3'): grViz names with quotes ────────────────────────
  Error in `ToDiagrammeRGraph(mytree)`: Package "DiagrammeR" is required to convert a `data.tree::Node`to a DiagrammeR graph. Please install it.
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-draw.R:144:3
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─data.tree::ToDiagrammeRGraph(mytree)
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 366 ]
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'shiny.semantic', 'knitr', 'rmarkdown', 'htmlwidgets'

Packages suggested but not available for checking:
  'covr', 'fixtuRes', 'lintr', 'spelling', 'targets', 'visNetwork'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'devtools', 'yaml'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("devtools")
  Error in library("devtools") : there is no package called 'devtools'
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'DT', 'datamods', 'htmlwidgets'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'shinytest2'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rgl', 'knitr', 'rmarkdown', 'ggExtra', 'plotly', 'htmlwidgets'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘DataVisualizations-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ROC
> ### Title: ROC plot
> ### Aliases: ROC
> 
> ### ** Examples
> 
> 
> Data = runif(1000,0,1)
> Cls  = sample(c(0,1), 1000, replace = TRUE)
> ROC(Data, Cls)
Loading required namespace: ROCit
Error in loadNamespace(x) : there is no package called ‘plotly’
Calls: ROC ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'gt', 'knitr', 'mediation', 'rmarkdown', 'rstanarm'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ryota Suzuki <suzuki@ef-prime.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ryota",
                    family = "Suzuki",
                    role = c("aut", "cre"),
                    email = "suzuki@ef-prime.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'DT', 'knitr', 'rmarkdown', 'shinytest2', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
  Running ‘test_zz.R’ [0s/1s]
  Running ‘testthat.R’ [6s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(datefixR)
  > 
  > test_check("datefixR")
  Starting 2 test processes.
  Saving _problems/test_fix_date_app-5.R
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 105 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test_app_1.R:5:3', 'test_app_1.R:83:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_fix_date_app.R:2:3'): unexpected theme raises error raises error ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `fix_date_app(theme = "test")`: The package "DT" is required to use `fix_date_app()`
  Backtrace:
      ▆
   1. ├─testthat::expect_error(fix_date_app(theme = "test"), "theme should be 'datefixR' or 'none' \n") at test_fix_date_app.R:2:3
   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. └─datefixR::fix_date_app(theme = "test")
   8.   └─rlang::check_installed(...)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 105 ]
  Deleting unused snapshots: 'mac-4.5/app_1/001.json', 'mac-4.5/app_1/001_.png',
  'mac-4.5/app_1/002-fixed.csv', 'mac-4.5/app_1/003.json',
  'mac-4.5/app_1/003_.png', 'shiny/app_1/001.json', 'shiny/app_1/001_.png',
  'shiny/app_1/002-fixed.csv', 'shiny/app_1/003.json', and 'shiny/app_1/003_.png'
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tim Bergsma <bergsmat@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tim",
                    family = "Bergsma",
                    role = c("aut", "cre"),
                    email = "bergsmat@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘yaml’

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘aoos’

Packages suggested but not available for checking:
  'lintr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Chris Hartgerink <chris@libscie.org>’

Found the following (possibly) invalid file URI:
  URI: CODE_OF_CONDUCT.md
    From: README.md
Package required but not available: ‘devtools’

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pkgdown', 'devtools', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘TSdist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rolf Turner <r.turner@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Rolf",
                    family = "Turner",
                    role = c("aut", "cre"),
                    email = "r.turner@auckland.ac.nz")
as necessary.
checkRd: (-1) plot.mleBb.Rd:48: Lost braces
    48 |   \ code{size} is extracted from argument \code{x}.
       |         ^
Maintainer: ‘Shaofeng Zhang <shaofeng.zhang@wmich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Joseph", "W."),
                      family = "McKean",
                      role = "aut"),
               person(given = "Shaofeng",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "shaofeng.zhang@wmich.edu"))
as necessary.
Package required but not available: ‘rmarkdown’

Package suggested but not available for checking: ‘knitr’

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gabriel Budel <gabysp_budel@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gabriel",
                      family = "Budel",
                      role = c("aut", "cre"),
                      email = "gabysp_budel@hotmail.com"),
               person(given = "Flavius",
                      family = "Frasincar",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("dbhydroR")
  Loading required package: dbhydroR
  Error in `source_dir()`:
  ! Failed to evaluate './setup-dbhydroR.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("dbhydroR")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at ./setup-dbhydroR.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<S3: packageNotFoundError>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'downlit', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'lintr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Nailong Zhang <setseed2016@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nailong",
                    family = "Zhang",
                    role = c("aut", "cre"),
                    email = "setseed2016@gmail.com")
as necessary.
Running examples in ‘dblr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dblr_train
> ### Title: Discrete Boosting Logistic Regression Training
> ### Aliases: dblr_train
> 
> ### ** Examples
> 
> # use iris data for example
> dat <- iris
> # create two categorical variables
> dat$Petal.Width <- as.factor((iris$Petal.Width<=0.2)*1+(iris$Petal.Width>1.0)*2)
> dat$Sepal.Length <- (iris$Sepal.Length<=3.0)*2+(iris$Sepal.Length>6.0)*1.25
> # create the response variable
> dat$Species <- as.numeric(dat$Species=='versicolor')
> set.seed(123)
> # random sampling
> index <- sample(1:150,100,replace = FALSE)
> # train the dblr model using the training data
> dblr_fit <- dblr_train(train_x=dat[index,c(1:4)],
+ train_y=dat[index,5],category_cols = c('Petal.Width','Sepal.Length'),
+ metric = 'logloss',subsample = 0.5,eta = 0.05,colsample = 1.0,
+ lambda = 1.0,cv_early_stops = 10,verbose=FALSE)
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: metrics. This warning will become an error in a future version.
Error in begin_iteration:end_iteration : argument of length 0
Calls: dblr_train -> <Anonymous>
Execution halted
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DiagrammeR'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘The Tien Mai <t.t.mai@medisin.uio.no>’

The Description field contains
  <arXiv:2103.11749>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) CI_mc.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{i}{the row index of the interest entry X_{i,j}}
       |                                                ^
checkRd: (-1) CI_mc.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{the row index of the interest entry X_{i,j}}
       |                                                ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Scott H. Koeneman <Scott.Koeneman@jefferson.edu>’

The Description field contains
  more information, see Koeneman and Cavanaugh (2023) <arXiv:2309.10614>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'pkgdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘bnviewer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'canvasXpress', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Packages required but not available: 'DT', 'leaflet', 'leaflet.extras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Timothy Conwell <timconwell@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Timothy",
                    family = "Conwell",
                    role = c("aut", "cre"),
                    email = "timconwell@gmail.com")
as necessary.
Maintainer: ‘Gokmen Altay <altaylabs@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gokmen",
                    family = "Altay",
                    role = c("aut", "cre"),
                    email = "altaylabs@gmail.com")
as necessary.
Maintainer: ‘Taiane Schaedler Prass <taianeprass@gmail.com>’

The Description field contains
  <arXiv:1910.10589>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Jonathan Berrisch <Jonathan@Berrisch.biz>’

The Description field contains
  distance correlation (see Chaudhuri, Hu (2019) <arXiv:1810.11332>
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) data.Rd:11: Lost braces
    11 | \doi{10.1007/s40258-021-00647-3}{DOI}
       |                                 ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Sharma Parichit <parishar@iu.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
No news entries found.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'DT', 'rlist', 'usethis'

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tensorflow’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Maria Dolores Martinez-Miranda <mmiranda@ugr.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Maria", "Dolores"),
                      family = "Martinez-Miranda",
                      role = c("aut", "cre"),
                      email = "mmiranda@ugr.es"),
               person(given = c("Jens", "Perch"),
                      family = "Nielsen",
                      role = "aut"),
               person(given = "Richard",
                      family = "Verrall",
                      role = "aut"))
as necessary.
Maintainer: ‘Virgilio Gómez-Rubio <Virgilio.Gomez@uclm.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Virgilio",
                      family = "Gómez-Rubio",
                      role = c("aut", "cre"),
                      email = "virgilio.gomez@uclm.es"),
               person(given = "Juan",
                      family = "Ferrándiz-Ferragud",
                      role = "aut"),
               person(given = "Antonio",
                      family = "López-Quílez",
                      role = "aut"),
               person(given = c("with", "contributions", "by", "Roger"),
                      family = "Bivand.",
                      role = "aut"))
as necessary.
Packages required but not available: 'yaml', 'validate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'cmdstanr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Dominic Edelmann <dominic.edelmann@dkfz-heidelberg.de>’

The Description field contains
  <arXiv:1808.07280>. Distance standard deviation methods (Edelmann, et
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Hang Weiqiang <e0010758@u.nus.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hang",
                    family = "Weiqiang",
                    role = c("aut", "cre"),
                    email = "e0010758@u.nus.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'gtsummary', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rifreg', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Zijian Guo <zijguo@stat.rutgers.edu>’

The Description field contains
  Debiased Lasso method was proposed in <arXiv:2004.03758>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [25s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ddml)
  > 
  > test_check("ddml")
  Saving _problems/test-ml_wrappers-35.R
  
  sample fold 1/3
  sample fold 2/3
  sample fold 3/3[ FAIL 1 | WARN 6 | SKIP 0 | PASS 134 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ml_wrappers.R:35:3'): mdl_xgboost is working ───────────────────
  Error in `process.y.margin.and.objective(as.vector(y), base_margin, objective, params)`: Got numeric 'y' - supported objectives for this data are: reg:squarederror, reg:squaredlogerror, reg:logistic, reg:pseudohubererror, reg:absoluteerror, reg:quantileerror, count:poisson, reg:gamma, reg:tweedie. Was passed: binary:logistic
  Backtrace:
      ▆
   1. └─ddml::mdl_xgboost(y, X, objective = "binary:logistic") at test-ml_wrappers.R:35:3
   2.   └─xgboost::xgboost(...)
   3.     └─xgboost:::process.y.margin.and.objective(...)
   4.       └─xgboost:::process.y.margin.and.objective(...)
  
  [ FAIL 1 | WARN 6 | SKIP 0 | PASS 134 ]
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tim Riffe <riffe@demogr.mpg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tim",
                      family = "Riffe",
                      role = c("aut", "cre"),
                      email = "riffe@demogr.mpg.de"),
               person(given = "Everton",
                      family = "Lima",
                      role = "aut"),
               person(given = "Bernardo",
                      family = "Queiroz",
                      role = "aut"))
as necessary.
checkRd: (-1) detectAgeInterval.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Age}, or code{age}.}
       |                                                                              ^
checkRd: (-1) detectSex.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Sex}, or code{sex}.}
       |                                                                              ^
checkRd: (-1) ggbgetAgesFit.Rd:28: Lost braces
    28 | code{\link{ggbChooseAges}}
       |     ^
Maintainer: ‘Fan Yang <fyang1@uchicago.edu>’

The Description field contains
  <arXiv:1906.00051>) by decomposing a large covariance matrix into a
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available: 'DT', 'mixtools'

Packages suggested but not available for checking:
  'ggExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘r2d3’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Xiaojie Qiu <xqiu@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xiaojie",
                      family = "Qiu",
                      role = c("aut", "cre"),
                      email = "xqiu@uw.edu"),
               person(given = "Cole",
                      family = "Trapnell",
                      role = "aut"),
               person(given = "Qi",
                      family = "Mao",
                      role = "aut"),
               person(given = "Li",
                      family = "Wang",
                      role = "aut"))
as necessary.
Specified C++11: support will be removed soon
Maintainer: ‘Hadrien Lorenzo <hadrien.lorenzo.2015@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hadrien",
                    family = "Lorenzo",
                    role = c("aut", "cre"),
                    email = "hadrien.lorenzo.2015@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Przemyslaw Biecek <przemyslaw.biecek@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Przemyslaw",
                      family = "Biecek",
                      role = c("aut", "cre"),
                      email = "przemyslaw.biecek@gmail.com",
                      comment = "R code"),
               person(given = "Teresa",
                      family = "Ledwina",
                      role = "aut",
                      comment = "support,\n    descriptions"))
as necessary.
Maintainer: ‘Mengbing Li <mengbing@umich.edu>’

The Description field contains
  <arXiv:2306.04700>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘ggtree’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Nunzio Torrisi <nunzio.torrisi@ieee.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nunzio",
                    family = "Torrisi",
                    role = c("aut", "cre"),
                    email = "nunzio.torrisi@ieee.org")
as necessary.
Maintainer: ‘Claus Dethlefsen <rpackage.deal@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Susanne", "Gammelgaard"),
                      family = "Bottcher",
                      role = "aut"),
               person(given = "Claus",
                      family = "Dethlefsen.",
                      role = "aut"),
               person(given = "Claus",
                      family = "Dethlefsen",
                      role = "cre",
                      email = "rpackage.deal@gmail.com"))
as necessary.
Packages required but not available: 'plotly', 'optiSolve'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Cameron M. Nugent <camnugent@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Cameron", "M."),
                    family = "Nugent",
                    role = c("aut", "cre"),
                    email = "camnugent@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Brendan Matthew Galdo <Brendan.m.galdo@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/bmgaldo/DEBBI
which should likely be
  https://github.com/bmgaldo/DEBBI/issues
instead.
Maintainer: ‘Hong Zhang <hzhang@wpi.edu>’

The Description field contains
  <arXiv:2401.00540>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Yikun Zhang <yikunzhang@foxmail.com>’

The Description field contains
  Giessing, and Chen (2023) <arXiv:2309.06429>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Philipp H Boersch-Supan <pboesu@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Specified C++14: support will be removed soon
Maintainer: ‘Christiana Kartsonaki <christiana.kartsonaki@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christiana",
                    family = "Kartsonaki",
                    role = c("aut", "cre"),
                    email = "christiana.kartsonaki@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Partha Sarathi Bishnu <psbishnu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Partha", "Sarathi"),
                    family = "Bishnu",
                    role = c("aut", "cre"),
                    email = "psbishnu@gmail.com")
as necessary.
Package required but not available: ‘chillR’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'CausalQueries', 'gam', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DeclareDesign)
  Loading required package: randomizr
  Loading required package: fabricatr
  Loading required package: estimatr
  > 
  > library(AER)
  Loading required package: car
  Loading required package: carData
  Loading required package: lmtest
  Loading required package: zoo
  
  Attaching package: 'zoo'
  
  The following objects are masked from 'package:base':
  
      as.Date, as.Date.numeric
  
  Loading required package: sandwich
  Loading required package: survival
  > library(betareg)
  > library(biglm)
  Loading required package: DBI
  > library(coin)
  
  Attaching package: 'coin'
  
  The following object is masked from 'package:testthat':
  
      expectation
  
  > library(future.apply)
  Loading required package: future
  
  Attaching package: 'future'
  
  The following object is masked from 'package:survival':
  
      cluster
  
  The following object is masked from 'package:lmtest':
  
      reset
  
  > library(gam)
  Error in library(gam) : there is no package called 'gam'
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'DT', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Neeraj Bokde <neerajdhanraj@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Neeraj",
                    family = "Bokde",
                    role = c("aut", "cre"),
                    email = "neerajdhanraj@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘usethis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) deconv.Rd:85: Lost braces; missing escapes or markup?
    85 |     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of {g}),
       |                                                           ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Matthias Bogaert <Matthias.Bogaert@UGent.Be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Matthias",
                    family = "Bogaert",
                    role = c("aut", "cre"),
                    email = "matthias.bogaert@ugent.be")
as necessary.
Packages required but not available: 'RWeka', 'RWekajars', 'rJava'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'JGR', 'rJava'

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mark van der Loo <mark.vanderloo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mark",
                      family = "van der Loo",
                      role = c("aut", "cre"),
                      email = "mark.vanderloo@gmail.com"),
               person(given = "Edwin",
                      family = "de Jonge",
                      role = "aut"),
               person(given = "Sander",
                      family = "Scholtus",
                      role = "aut"))
as necessary.
Package required but not available: ‘validate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'rmarkdown', 'spelling', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Suren Rathnayake <surenr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Cinzia",
                      family = "Viroli",
                      role = "aut"),
               person(given = c("Geoffrey", "J."),
                      family = "McLachlan",
                      role = "aut"),
               person(given = "Suren",
                      family = "Rathnayake",
                      role = "cre",
                      email = "surenr@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'SuperLearner', 'keras3', 'Hmisc'

Packages suggested but not available for checking: 'gam', 'tensorflow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Xiao Rong <runxiao@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Xiao",
                    family = "Rong",
                    role = c("aut", "cre"),
                    email = "runxiao@gmail.com")
as necessary.
checkRd: (-1) deepNN-package.Rd:18: Lost braces
    18 | section{Dependencies}{
       |        ^
checkRd: (-1) deepNN-package.Rd:18-21: Lost braces
    18 | section{Dependencies}{
       |                      ^
checkRd: (-1) deepNN-package.Rd:23: Lost braces
    23 | section{Citation}{
       |        ^
checkRd: (-1) deepNN-package.Rd:23-25: Lost braces
    23 | section{Citation}{
       |                  ^
checkRd: (-1) deepNN-package.Rd:27-38: Lost braces
    27 | references{
       |           ^
Maintainer: ‘Brian <bleemayer@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Brian", "Lee"),
                      family = "Mayer",
                      role = "aut"),
               person(family = "Brian",
                      role = "cre",
                      email = "bleemayer@gmail.com"))
as necessary.
Packages required but not available: 'keras', 'tensorflow'

Packages suggested but not available for checking:
  'covr', 'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tensorflow', 'tfprobability', 'keras', 'tfruns'

Packages suggested but not available for checking: 'knitr', 'covr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'ggtree', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'tensorflow', 'keras', 'tfprobability', 'deepregression'

Packages suggested but not available for checking: 'knitr', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Javaria Ahmad Khan <jakhan0@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Javaria", "Ahmad"),
                      family = "Khan",
                      role = c("aut", "cre"),
                      email = "jakhan0@yahoo.com"),
               person(given = "Atif",
                      family = "Akbar.",
                      role = "aut"))
as necessary.
Maintainer: ‘Nick Golding <nick.golding.research@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nick",
                    family = "Golding",
                    role = c("aut", "cre"),
                    email = "nick.golding.research@gmail.com")
as necessary.
Maintainer: ‘Toshihiro Umehara <toshi@niceume.com>’

The BugReports field in DESCRIPTION has
  https://github.com/niceume/defineOptions
which should likely be
  https://github.com/niceume/defineOptions/issues
instead.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘defineOptions-package.Rd’ ‘define_option.Rd’ ‘parse_with_defs.Rd’
    ‘summary.parsed_result.Rd’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(deflist)
  > 
  > test_check("deflist")
  Loading required namespace: digest
  Failed with error:  'there is no package called 'digest''
  Saving _problems/test_deflist-22.R
  Loading required namespace: digest
  Failed with error:  'there is no package called 'digest''
  Saving _problems/test_deflist-86.R
  Loading required namespace: digest
  Failed with error:  'there is no package called 'digest''
  Saving _problems/test_deflist-112.R
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 23 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_deflist.R:22:3'): can create a memoised deflist ────────────────
  Error in `cache_memory()`: Package `digest` must be installed for `cache_memory()`.
  Backtrace:
      ▆
   1. └─deflist::deflist(function(i) i, len = 10, memoise = TRUE) at test_deflist.R:22:3
   2.   └─memoise::cache_memory()
  ── Error ('test_deflist.R:86:3'): deflist memoisation works ────────────────────
  Error in `cache_memory()`: Package `digest` must be installed for `cache_memory()`.
  Backtrace:
      ▆
   1. └─deflist::deflist(square_fun, len = 5, memoise = TRUE) at test_deflist.R:86:3
   2.   └─memoise::cache_memory()
  ── Error ('test_deflist.R:112:3'): deflist file cache works ────────────────────
  Error in `memoise::cache_filesystem(cachedir)`: Package `digest` must be installed for `cache_filesystem()`.
  Backtrace:
      ▆
   1. └─deflist::deflist(...) at test_deflist.R:112:3
   2.   └─memoise::cache_filesystem(cachedir)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 23 ]
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘StableEstim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: support will be removed soon
Maintainer: ‘Philippe Lambert <p.lambert@uliege.be>’

The Description field contains
  (2021) <arXiv:2107.03883> for details.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'BiocStyle'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'yaml', 'lemon'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/UserGuide.Rnw’
   ‘inst/doc/analysingExistingDatasets.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Bill Wheeler <wheelerb@imsweb.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhenzhen",
                      family = "Xu",
                      role = "aut",
                      email = "Zhenzhen.Xu@fda.hhs.gov"),
               person(given = "Boguang",
                      family = "Zhen",
                      role = "aut",
                      email = "Boguang.Zhen@fda.hhs.gov"),
               person(given = "Yongsoek",
                      family = "Park",
                      role = "aut",
                      email = "yongpark@pitt.edu"),
               person(given = "Bin",
                      family = "Zhu",
                      role = "aut",
                      email = "bin.zhu@nih.gov"),
               person(given = "Bill",
                      family = "Wheeler",
                      role = "cre",
                      email = "wheelerb@imsweb.com"))
as necessary.
Package required but not available: ‘visNetwork’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Rolf Turner <rolfturner@posteo.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Rolf",
                    family = "Turner",
                    role = c("aut", "cre"),
                    email = "rolfturner@posteo.net")
as necessary.
Package required but not available: ‘ggtree’

Packages suggested but not available for checking:
  'bGMYC', 'knitr', 'splits', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David Magis <david.magis@ulg.ac.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Magis",
                      role = c("aut", "cre"),
                      email = "david.magis@ulg.ac.be",
                      comment = "U Liege"),
               person(given = "Bruno",
                      family = "Facon",
                      role = "aut",
                      comment = "Univ Lille-Nord de France"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) deltaPlot.Rd:28: Lost braces
    28 |  \item{purify}{logical: should item purification be performed? (Default is code{FALSE}). See \bold{Details}.}
       |                                                                                ^
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
Maintainer: ‘Javaria Ahmad Khan <jakhan0@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Javaria", "Ahmad"),
                      family = "Khan",
                      role = c("aut", "cre"),
                      email = "jakhan0@yahoo.com"),
               person(given = "Atif",
                      family = "Akbar.",
                      role = "aut"))
as necessary.
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Terry Therneau <therneau.terry@mayo.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Terry",
                    family = "Therneau",
                    role = c("aut", "cre"),
                    email = "therneau.terry@mayo.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Caswell.R’
Found the following files/directories:
  ‘smd_table.docx’
Package required but not available: ‘flextable’

Packages suggested but not available for checking:
  'knitr', 'quarto', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘quarto’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Hana Sevcikova <hanas@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("James", "Holland"),
                      family = "Jones",
                      role = "aut",
                      email = "jhj1@stanford.edu"),
               person(given = "Jim",
                      family = "Oeppen",
                      role = "ctb"),
               person(given = "Hana",
                      family = "Sevcikova",
                      role = "cre",
                      email = "hanas@uw.edu"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Bill Venables <Bill.Venables@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bill",
                    family = "Venables",
                    role = c("aut", "cre"),
                    email = "bill.venables@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) kin.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:53-61: Lost braces
    53 | {\itemize{
       | ^
checkRd: (-1) kin.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:59-67: Lost braces
    59 | {\itemize{
       | ^
checkRd: (-1) kin2sex.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Vinca Prana <vinca.prana@free.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Vinca",
                    family = "Prana",
                    role = c("aut", "cre"),
                    email = "vinca.prana@free.fr")
as necessary.
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'heatmaply', 'covr'

Packages which this enhances but not available for checking:
  'Hmisc', 'WGCNA'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tidyverse’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gregory Jefferis <jefferis@gmail.com>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘dendroextras-package.Rd’:
    \keyword{package,}
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DiagrammeR'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'plotly'

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Catherine Hurley <catherine.hurley@mu.ie>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Catherine", "B."),
                      family = "Hurley",
                      role = "aut"),
               person(given = "Denise",
                      family = "Earle",
                      role = "aut"),
               person(given = "Catherine",
                      family = "Hurley",
                      role = "cre",
                      email = "catherine.hurley@mu.ie"))
as necessary.
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
'library' or 'require' calls not declared from:
  ‘HSAUR2’ ‘Iyer517’ ‘PairViz’ ‘RColorBrewer’ ‘mvtnorm’ ‘scagnostics’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tabulapdf’

Package suggested but not available for checking: ‘roxygen2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'tidyverse', 'DiagrammeR'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘James Ware <j.ware@imperial.ac.uk>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘fmrpGenes.Rd’:
    http://dx.doi.org/10.1016/j.cell.2011.06.013
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Matt P. Wand <matt.wand@uts.edu.au>’

The Description field contains
  methodology is described in Wand and Yu (2020) <arXiv:2009.06182>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [168s/50s]
Running R code in ‘testthat.R’ had CPU time 3.4 times elapsed time
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yikai Wang <johnzon.wyk@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yikai",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "johnzon.wyk@gmail.com"),
               person(given = "Jian",
                      family = "Kang",
                      role = "aut"),
               person(given = c("Phebe", "Brenne"),
                      family = "Kemmer",
                      role = "aut"),
               person(given = "Ying",
                      family = "Guo",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘flextable’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Carl A. B. Pearson <carl.pearson@lshtm.ac.uk>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘denvax.Rd’:
    https://doi.org/10.1098/rsif.2019.0234
  File ‘lazou2016.Rd’:
    https://doi.org/10.1056/NEJMoa1503877
  File ‘morrison2010.Rd’:
    https://doi.org/10.1371/journal.pntd.0000670
  File ‘nPxA.Rd’:
    https://doi.org/10.1098/rsif.2019.0234
Cannot process vignettes
Packages suggested but not available for checking:
  'usethis', 'devtools', 'roxygen2', 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Katharine Mullen <mullenkate@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Eckhard Liebscher <eckhard.liebscher@hs-merseburg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Eckhard",
                    family = "Liebscher",
                    role = c("aut", "cre"),
                    email = "eckhard.liebscher@hs-merseburg.de")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Takeshi Emura <takeshiemura@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Takeshi",
                    family = "Emura",
                    role = c("aut", "cre"),
                    email = "takeshiemura@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'plotly', 'rmarkdown', 'htmlwidgets'

Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Aurora Torrente <etorrent@est-econ.uc3m.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sara",
                      family = "Lopez-Pintado",
                      role = "aut",
                      email = "sl2929@columbia.edu"),
               person(given = "Aurora",
                      family = "Torrente.",
                      role = "aut",
                      email = "etorrent@est-econ.uc3m.es"),
               person(given = "Aurora",
                      family = "Torrente",
                      role = "cre",
                      email = "etorrent@est-econ.uc3m.es"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'bookdown'
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Francisco Parra  <parra_fj@cantabria.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Francisco",
                    family = "Parra",
                    role = c("aut", "cre"),
                    email = "parra_fj@cantabria.es")
as necessary.
Package required but not available: ‘fNonlinear’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘descriptio-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contab
> ### Title: Bivariate statistics between a continuous variable and a set of
> ###   variables
> ### Aliases: contab
> ### Keywords: multivariate misc
> 
> ### ** Examples
> 
> data(Movies)
> contab(x = Movies[, c("Genre", "ArtHouse", "Budget")],
+        y = Movies$BoxOffice)
Error in contab(x = Movies[, c("Genre", "ArtHouse", "Budget")], y = Movies$BoxOffice) : 
  gt package should be installed to use this function
Execution halted
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jakson Aquino <jalvesaq@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jakson", "Aquino.", "Includes", "R", "source", "code", "and/or", "documentation", "written", "by", "Dirk"),
                      family = "Enzmann",
                      role = "aut"),
               person(given = "Marc",
                      family = "Schwartz",
                      role = "aut"),
               person(given = "Nitin",
                      family = "Jain",
                      role = "aut"),
               person(given = "Stefan",
                      family = "Kraft",
                      role = "aut"),
               person(given = "Jakson",
                      family = "Aquino",
                      role = "cre",
                      email = "jalvesaq@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Harish Kumar <kadamatiharish@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Harish",
                    family = "Kumar",
                    role = c("aut", "cre"),
                    email = "kadamatiharish@gmail.com")
as necessary.
Package required but not available: ‘DT’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

Packages suggested but not available for checking:
  'knitr', 'lintr', 'rmarkdown', 'shinytest2'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'pkgdown', 'knitr', 'rmarkdown', 'gt', 'tidyverse',
  'printr', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Max Kuhn <mxkuhn@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Max",
                    family = "Kuhn",
                    role = c("aut", "cre"),
                    email = "mxkuhn@gmail.com")
as necessary.
Maintainer: ‘Stanley E. Lazic <stan.lazic@cantab.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Stanley", "E."),
                    family = "Lazic",
                    role = c("aut", "cre"),
                    email = "stan.lazic@cantab.net")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Robert Adamek <robertadamek94@gmail.com>’

The Description field contains
  covariance estimator in Adamek et al. (2020) <arXiv:2007.10952>. Also
  as described in Adamek et al. (2022) <arXiv:2209.03218>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
'library' or 'require' call not declared from: ‘nlme’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Norm Matloff <normmatloff@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Norm",
                    family = "Matloff",
                    role = c("aut", "cre"),
                    email = "normmatloff@gmail.com")
as necessary.
Package required but not available: ‘knitr’

Packages suggested but not available for checking: 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'kableExtra'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Daniel Meyer <meyerda@ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Daniel",
                    family = "Meyer",
                    role = c("aut", "cre"),
                    email = "meyerda@ethz.ch")
as necessary.

The Description field contains
  see: Meyer, D.W. (2016) <arXiv:1610.00345> or Meyer, D.W., Statistics
  (2017) <arXiv:1711.04632> or Meyer, D.W., Journal of Computational and
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘det.construct.Rd’:
    https://doi.org/10.1007/s11222-017-9751-9
  File ‘detpack.Rd’:
    https://doi.org/10.1007/s11222-017-9751-9
    https://doi.org/10.1080/10618600.2018.1482768
Maintainer: ‘Filipe Campelo <fcampelo@ci.uc.pt>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Filipe",
                    family = "Campelo",
                    role = c("aut", "cre"),
                    email = "fcampelo@ci.uc.pt")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Guangsheng Pei <peiguangsheng@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Guangsheng",
                    family = "Pei",
                    role = c("aut", "cre"),
                    email = "peiguangsheng@gmail.com")
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘deTS-package.Rd’:
    \keyword{ deTS; TSEA }
Maintainer: ‘Magnus Kristoffersen <magnus.kristoffersen@geo.uio.no>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘DT’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Robin Van Oirbeek <robin.vanoirbeek@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Robin",
                    family = "Van Oirbeek",
                    role = c("aut", "cre"),
                    email = "robin.vanoirbeek@gmail.com")
as necessary.
Maintainer: ‘John Verzani <jverzani@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Original", "by", "Jay", "L."),
                      family = "Devore",
                      role = "aut"),
               person(given = c("modifications", "by", "Douglas"),
                      family = "Bates",
                      role = "aut",
                      email = "bates@stat.wisc.edu"),
               person(given = c("modifications", "for", "7th", "edition", "by", "John"),
                      family = "Verzani.",
                      role = "aut"),
               person(given = "John",
                      family = "Verzani",
                      role = "cre",
                      email = "jverzani@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'usethis', 'pkgdown', 'profvis', 'roxygen2'

Packages suggested but not available for checking:
  'covr', 'DT', 'knitr', 'lintr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'DT', 'networkD3'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘yaml’

Packages suggested but not available for checking:
  'rmarkdown', 'prettydoc', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Victor Barreto Mesquita <victormesquita40@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Victor", "Barreto"),
                      family = "Mesquita",
                      role = c("ctb", "aut", "cre"),
                      email = "victormesquita40@hotmail.com"),
               person(given = c("Florêncio", "Mendes", "Oliveira"),
                      family = "Filho",
                      role = c("ctb", "aut")),
               person(given = c("Ian", "Meneghel"),
                      family = "Danilevicz.",
                      role = c("ctb", "aut")))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Shawn Waldroff <swaldroff@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Shawn",
                    family = "Waldroff",
                    role = c("aut", "cre"),
                    email = "swaldroff@gmail.com")
as necessary.
Maintainer: ‘Jimmy Duong <jkd2108@columbia.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ken",
                      family = "Cheung",
                      role = "aut",
                      email = "yc632@columbia.edu"),
               person(given = "Jimmy",
                      family = "Duong",
                      role = "cre",
                      email = "jkd2108@columbia.edu"))
as necessary.
Packages required but not available:
  'signatureSearch', 'signatureSearchData', 'gprofiler2'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'quarto'

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Victor H. Cervantes <vhcervantesb@unal.edu.co>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Victor", "H."),
                    family = "Cervantes",
                    role = c("aut", "cre"),
                    email = "vhcervantesb@unal.edu.co")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ravi Varadhan <ravi.varadhan@jhu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ravi",
                      family = "Varadhan",
                      role = c("aut", "cre"),
                      email = "ravi.varadhan@jhu.edu"),
               person(given = c("Johns", "Hopkins"),
                      family = "University"),
               person(given = c("Hans", "W."),
                      family = "Borchers",
                      role = "aut"),
               person(given = c("ABB", "Corporate"),
                      family = "Research"),
               person(given = "Vincent",
                      family = "Bechard",
                      role = "aut"),
               person(given = "HEC",
                      family = "Montreal",
                      comment = "Montreal University"))
as necessary.
Maintainer: ‘Leihong Wu <leihong.wu@fda.hhs.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Leihong",
                      family = "Wu",
                      role = c("aut", "cre"),
                      email = "leihong.wu@fda.hhs.gov"),
               person(given = "Weida",
                      family = "Tong",
                      role = "aut",
                      comment = "Weida.tong@fda.hhs.gov"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Giovanna Capizzi <giovanna.capizzi@unipd.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Giovanna",
                      family = "Capizzi",
                      role = c("aut", "cre"),
                      email = "giovanna.capizzi@unipd.it"),
               person(given = "Guido",
                      family = "Masarotto",
                      role = "aut"))
as necessary.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Shipei Zeng <shipei.zeng@unswalumni.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Shipei",
                    family = "Zeng",
                    role = c("aut", "cre"),
                    email = "shipei.zeng@unswalumni.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Nicolae Teodor Melita <nt_melita@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Nicolae", "Teodor"),
                    family = "Melita",
                    role = c("aut", "cre"),
                    email = "nt_melita@yahoo.com")
as necessary.
Package required but not available: ‘MLInterfaces’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'canvasXpress', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) runContrasts.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:82: Lost braces in \itemize; meant \describe ?