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install log '' does not exist
installed size is 17.6Mb
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installed size is 12.0Mb
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    doc    3.9Mb
    libs   7.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
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GNU make is a SystemRequirements.
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    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
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GNU make is a SystemRequirements.
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installed size is  7.1Mb
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    data   4.6Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
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    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
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Malformed Description field: should contain one or more complete sentences.
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calculate_mean_linear_projection: no visible binding for global
  variable 'id'
calculate_within_between_terms: no visible binding for global variable
  'id'
create_cohort: no visible binding for global variable 'id'
Undefined global functions or variables:
  id
'LazyData' is specified without a 'data' directory
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    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
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    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
Package which this enhances but not available for checking: 'sl3'
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
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No news entries found.
Error(s) in re-building vignettes:
--- re-building 'neun_euro_ticket_demonstrator.Rmd' using rmarkdown
--- finished re-building 'neun_euro_ticket_demonstrator.Rmd'

--- re-building 'user_sample_1.Rmd' using rmarkdown
File figure/plot_counter_1-1.png not found in resource path
Error: processing vignette 'user_sample_1.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'user_sample_1.Rmd'

--- re-building 'user_sample_2.Rmd' using rmarkdown
--- finished re-building 'user_sample_2.Rmd'

--- re-building 'user_sample_3.Rmd' using rmarkdown
File figure/bias_plot-1.png not found in resource path
Error: processing vignette 'user_sample_3.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'user_sample_3.Rmd'

SUMMARY: processing the following files failed:
  'user_sample_1.Rmd' 'user_sample_3.Rmd'

Error: Vignette re-building failed.
Execution halted
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GNU make is a SystemRequirements.
installed size is  8.6Mb
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Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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installed size is 12.1Mb
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    42 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
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    33 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
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installed size is 18.8Mb
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    libs  14.9Mb
GNU make is a SystemRequirements.
installed size is  8.1Mb
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    doc   7.6Mb
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Package suggested but not available for checking: 'USA.state.boundaries.data'
installed size is  6.1Mb
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    doc   3.8Mb
installed size is  9.9Mb
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    extdata   9.8Mb
installed size is  7.0Mb
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    data   6.9Mb
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installed size is 24.5Mb
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    doc    1.8Mb
    libs  22.5Mb
Problems with news in 'NEWS.md':
No news entries found.
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Packages suggested but not available for checking: 'vaers', 'vaersND'
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checkRd: (-1) sample_gen.Rd:18: Lost braces; missing escapes or markup?
    18 | Generate \code{n} random samples from multivariate Gaussian distribution N(0, (L^TL)^{-1})
       |                                                                                      ^
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checkRd: (-1) vardannual.Rd:97: Lost braces
    97 | \item{ID_level2}{Optional}{variable for unit ID codes. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                           ^
checkRd: (-1) vardannual.Rd:99: Lost braces
    99 | \item{dataset}{Optional}{survey data object convertible to \code{data.table}.}
       |                         ^
checkRd: (-1) vardcrospoor.Rd:122: Lost braces
   122 | \item{ind_gr}{Optional}{variable by which divided independently X matrix of the auxiliary variables for the calibration. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                        ^
checkRd: (-1) vardcrospoor.Rd:124: Lost braces
   124 | \item{use.estVar}{Logical}{value. If value is \code{TRUE}, then \code{R} function \code{estVar} is used for the  estimation of covariance matrix of the residuals. If value is \code{FALSE}, then \code{R} function \code{estVar} is not used for the estimation of covariance matrix of the residuals.}
       |                           ^
checkRd: (-1) vardom_othstr.Rd:69: Lost braces
    69 | \item{percentratio}{Positive}{numeric value. All linearized variables are multiplied with \code{percentratio} value, by default - 1.}
       |                              ^
checkRd: (-1) varpoord.Rd:121: Lost braces
   121 | \item{month_at_work}{Variable}{for total number of month at work (sum of the number of months spent at full-time work as employee, number of months spent at part-time work as employee, number of months spent at full-time work as self-employed (including family worker), number of months spent at part-time work as self-employed (including family worker)).  One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                               ^
'LazyData' is specified without a 'data' directory
Running examples in 'vardpoor-Ex.R' failed
The error most likely occurred in:

> ### Name: vardannual
> ### Title: Variance estimation for measures of annual net change or annual
> ###   for single and multistage stage cluster sampling designs
> ### Aliases: vardannual
> ### Keywords: vardannual
> 
> ### ** Examples
> 
>  
> ### Example
> library("data.table")
> 
> set.seed(1)
> 
> data("eusilc", package = "laeken")
> eusilc1 <- eusilc[1:20, ]
> rm(eusilc)
> 
> dataset1 <- data.table(rbind(eusilc1, eusilc1),
+                        year = c(rep(2010, nrow(eusilc1)),
+                                 rep(2011, nrow(eusilc1))))
> rm(eusilc1)
> 
> dataset1[, country := "AT"]
> dataset1[, half := .I - 2 * trunc((.I - 1) / 2)]
> dataset1[, quarter := .I - 4 * trunc((.I - 1) / 4)]
> dataset1[age < 0, age := 0]
> 
> PSU <- dataset1[, .N, keyby = "db030"][, N := NULL][]
> PSU[, PSU := trunc(runif(.N, 0, 5))]
> 
> dataset1 <- merge(dataset1, PSU, all = TRUE, by = "db030")
> rm(PSU)
> 
> dataset1[, strata := "XXXX"]
> dataset1[, employed := trunc(runif(.N, 0, 2))]
> dataset1[, unemployed := trunc(runif(.N, 0, 2))]
> dataset1[, labour_force := employed + unemployed]
> dataset1[, id_lv2 := paste0("V", .I)]
> 
> vardannual(Y = "employed", H = "strata",
+            PSU = "PSU", w_final = "rb050",
+            ID_level1 = "db030", ID_level2 = "id_lv2",
+            Dom = NULL, Z = NULL, years = "year",
+            subperiods = "half", dataset = dataset1,
+            percentratio = 100, confidence = 0.95,
+            method = "cros")
Error in t(X) %*% A_matrix : non-conformable arguments
Calls: vardannual -> lapply -> FUN -> data.table
Execution halted
checkRd: (-1) betaburr.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Burr distribution due to Parana\'{i}ba et al. (2011) given by
       |                                                                                                                        ^
checkRd: (-1) betafrechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Fr\'{e}chet distribution due to Barreto-Souza et al. (2011) given by
       |                                                                                           ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                      ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                                                      ^
checkRd: (-1) kumburr7.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Kumaraswamy Burr XII distribution due to Parana\'{i}ba et al. (2013) given by
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
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    40 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + exp(2*X22)*e
       |                                ^
checkRd: (-1) simulateDCSIS.Rd:42: Lost braces
    42 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + 6*X22 + e
       |                                ^
'LazyData' is specified without a 'data' directory
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    15 | \item{file.suffix}{Regex expression for end of file name. For example, `file.suffix = '_S\\d{1,2}_.*_R1_.*'` will match R1 files.1 files.}
       |                                                                                             ^
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checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
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GNU make is a SystemRequirements.
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    help   3.3Mb
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get_source_ids: no visible binding for global variable 'id'
Undefined global functions or variables:
  id
checkRd: (-1) VirtualArray-single-bracket-method.Rd:6: Lost braces
     6 | \title{Indexing to extract subsets of a 'code{\link[via:XArray-class]{VirtualArray}}'-class object}
       |                                              ^
checkRd: (-1) subset.Rd:20: Lost braces
    20 | \item{drop}{\code{logical} in case the result of subsetting is a single element, should the \\code{\link[via:XArray-class]{VirtualArray}} wrapper be dropped?}
       |                                                                                                   ^
installed size is 10.8Mb
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   311 | albedo must be supplied in code{forcing_veg}. Default = 1.}
       |                                ^
checkRd: (-1) vic_param.Rd:323: Lost braces
   323 | supplied in code{forcing_veg}. Default = 1.}
       |                 ^
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   341 | be supplied in code{forcing_veg} Default = 0.}
       |                    ^
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'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     22.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Data-Examples.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aquaporin.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:34: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) WACS.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACSreadAgroclim.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) WACSreadAgroclim.Rd:16-17: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   4.4Mb
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    sample_data  27.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'prepr'
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) busTrace.Rd:15: Lost braces
    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
checkRd: (-1) WeightedROC.Rd:10: Lost braces; missing escapes or markup?
    10 | integer/numeric with values all in {0=negative,1=positive} or
       |                                    ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       | ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       |                            ^
checkRd: (-1) CLIC.Rd:149: Lost braces
   149 | Composite likelihood {E}{M} algorithm with applications to
       |                         ^
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc   7.5Mb
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [395s]
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(whirl)
  > 
  > test_check("whirl")
  Saving _problems/test-mdformats-35.R
  
                              
  [ FAIL 1 | WARN 0 | SKIP 16 | PASS 150 ]
  
  ══ Skipped tests (16) ══════════════════════════════════════════════════════════
  • On CRAN (16): 'test-biocompute.R:1:1', 'test-custom_logging.R:19:1',
    'test-examples.R:2:3', 'test-python.R:2:3', 'test-python.R:44:3',
    'test-run.R:33:3', 'test-run.R:76:3', 'test-run.R:87:3', 'test-run.R:95:3',
    'test-run.R:112:3', 'test-run.R:134:3', 'test-run.R:151:3',
    'test-run.R:161:3', 'test-strace.R:42:3', 'test-util_queue_summary.R:11:3',
    'test-whirl_queue.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-mdformats.R:29:3'): pandoc works ─────────────────────────────
  Expected `all(...)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 1 | WARN 0 | SKIP 16 | PASS 150 ]
  Error:
  ! Test failures.
  Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   3.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) milakes.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:22: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  stop.c:10:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/winch.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
checkRd: (-1) secondDerivative.Rd:14: Lost braces
    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
checkRd: (-1) windAC.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:33: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
--- re-building 'wlsd.Rmd' using rmarkdown
Error reading bibliography file wlsd.bib:
(line 70, column 31):
unexpected '%'
expecting white space
Error: processing vignette 'wlsd.Rmd' failed with diagnostics:
pandoc document conversion failed with error 25
--- failed re-building 'wlsd.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'wordnetDicts'
checkRd: (-1) wordpiece_cache_dir.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wordpiece_cache_dir.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wordpiece_cache_dir.Rd:20-21: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
Package suggested but not available for checking: 'wmtsa'
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'tidyr'
A package should be listed in only one of these fields.
Missing or unexported object: 'CVXR::diff'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   2.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.9Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'GenerateModelCN.Rmd' using rmarkdown
File Wb.png not found in resource path
Error: processing vignette 'GenerateModelCN.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'GenerateModelCN.Rmd'

--- re-building 'GenerateModelCP.Rmd' using rmarkdown
File Wc.png not found in resource path
Error: processing vignette 'GenerateModelCP.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'GenerateModelCP.Rmd'

--- re-building 'GenerateModelP.Rmd' using rmarkdown
File Wa.png not found in resource path
Error: processing vignette 'GenerateModelP.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'GenerateModelP.Rmd'

--- re-building 'GenerateModelPC.Rmd' using rmarkdown
File Wd.png not found in resource path
Error: processing vignette 'GenerateModelPC.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'GenerateModelPC.Rmd'

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

--- re-building 'WsMed.Rmd' using rmarkdown
File Wa.png not found in resource path
Error: processing vignette 'WsMed.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'WsMed.Rmd'

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

SUMMARY: processing the following files failed:
  'GenerateModelCN.Rmd' 'GenerateModelCP.Rmd' 'GenerateModelP.Rmd'
  'GenerateModelPC.Rmd' 'WsMed.Rmd'

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) wtest.Rd:61-64: Lost braces
    61 | {When \code{w.order} =2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) wtest.high.Rd:61-64: Lost braces
    61 | {When \code{w.order} > 2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) exploreSignatures.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:67-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateData.Rd:47: Lost braces
    47 | \bold{code{data}} \tab the generated data \cr
       |           ^
checkRd: (-1) generateData.Rd:53: Lost braces
    53 | Refer to \bold{\emph{code{\link{retrieveDataFactory}}}} and to
       |                          ^
checkRd: (-1) qualifyFunctionArguments.Rd:14: Lost braces
    14 | A emph{\code{list}} with following names
       |       ^
checkRd: (-1) qualifyFunctionArguments.Rd:26: Lost braces
    26 | \item{code{arguments}}{a \code{pairList} of argument names and values.
       |           ^
checkRd: (-1) completeManualPage.Rd:12: Lost braces
    12 | See \emph{\bold{code{\link{ProcessingContext}}}}. Only
       |                     ^
checkRd: (-1) produceAllManualPagesFromObject.Rd:14: Lost braces
    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
checkRd: (-1) chemnet.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chemnet.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:105: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    java  26.7Mb
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    java  11.7Mb
checkRd: (-1) xml_to_df.Rd:144: Lost braces; missing escapes or markup?
   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: namespace 'nlmixr2est' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/4.4/xpose.xtras.Rcheck/00install.out' for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    3.2Mb
Running examples in 'xpose.xtras-Ex.R' failed
The error most likely occurred in:

> ### Name: backfill_nlmixr2_props
> ### Title: Populate some properties from nlmixr2 fit
> ### Aliases: backfill_nlmixr2_props
> 
> ### ** Examples
> 
> 
> xpdb_nlmixr2 %>%
+   set_prop(condn = "not implemented") %>%
+   get_prop("condn")
[1] "not implemented"
> 
> xpdb_nlmixr2 %>%
+   set_prop(condn = "not implemented") %>%
+   backfill_nlmixr2_props() %>%
+   get_prop("condn")
Error in `backfill_nlmixr2_props()`:
! Incompatible nlmixr2/rxode2 fit object detected
ℹ This object was created with rxode2 < 5.0 and cannot be used with rxode2 >= 5.0
✖ The internal rxUi structure is incompatible between versions
! Please regenerate the fit object using current versions of nlmixr2est and rxode2
Backtrace:
    ▆
 1. ├─... %>% get_prop("condn")
 2. ├─xpose.xtras::get_prop(., "condn")
 3. │ └─xpose::get_summary(xpdb)
 4. │   └─xpose::check_xpdb(xpdb, check = "summary")
 5. │     └─xpose::is.xpdb(xpdb)
 6. └─xpose.xtras::backfill_nlmixr2_props(.)
 7.   └─rlang::abort(...)
Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [338s]
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(xpose.xtras)
  ℹ xpose is not currently attached.
  
  Attaching package: 'xpose.xtras'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("xpose.xtras")
  Saving _problems/test-nlmixr2-10.R
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 847 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-covariates.R:123:3', 'test-xplot_boxplot.R:157:3',
    'test-xplot_pairs.R:44:3', 'test-xset_features.R:170:3',
    'test-xset_features.R:170:3', 'test-xset_features.R:170:3',
    'test-xset_features.R:170:3'
  • requireNamespace("rxode2", quietly = TRUE) && "rxDerived" %in%
    getNamespaceExports("rxode2") is TRUE (2): 'test-diag_constants.R:123:3',
    'test-diag_constants.R:129:3'
  • {qs} is not installed (1): 'test-nlmixr2.R:317:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-nlmixr2.R:8:3'): old fit detection works correctly ───────────
  Expected `test_nlmixr2_is_old_fit(xpdb_nlmixr2)` to be FALSE.
  Differences:
  `actual`:   TRUE 
  `expected`: FALSE
  
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 847 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) xwfGridsearch.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{iter}{Number of levels in the adaptive grid search. The resolution in b obtained is 2^{-1-iter}.}
       |                                                                                             ^
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.1Mb
Package suggested but not available for checking: 'MBESS'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
calculationAlphaHelix: no visible binding for global variable 'id'
calculationBetaSheet: no visible binding for global variable 'id'
calculationChain: no visible binding for global variable 'id'
Undefined global functions or variables:
  id
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) glm.cons.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{method}{the method used in fitting the model. The default method "\code{glm.fit.cons}" uses function {nnnpls} from package nnls instead of \code{lm.fit} to impose the sign of the coefficients. As in \code{glm}, the alternative method "\code{model.frame}" returns the model frame and does no fitting.}
       |                                                                                                            ^
Running examples in 'zetadiv-Ex.R' failed
The error most likely occurred in:

> ### Name: Zeta.order.ex
> ### Title: Expectation of zeta diversity for a specific number of
> ###   assemblages or sites
> ### Aliases: Zeta.order.ex
> 
> ### ** Examples
> 
> 
> utils::data(bird.spec.coarse)
> data.spec.bird <- bird.spec.coarse[,3:193]
> 
> zeta.bird <- Zeta.order.ex(data.spec.bird, order = 3)
> zeta.bird
$zeta.order
[1] 3

$combinations
[1] 302621

$zeta.val
[1] 57.61204

$zeta.val.sd
[1] 13.10351

> 
> ##########
> s
Error: object 's' not found
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:182: Lost braces
   182 |   dQuote{tab-delimited text file} when you have done and close the spreadsheet
       |         ^
checkRd: (-1) in.zoom.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_ztable.Rd:75: Lost braces; missing escapes or markup?
    75 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.}
       |                                          ^
checkRd: (-1) ztable_sub.Rd:78: Lost braces; missing escapes or markup?
    78 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.
       |                                          ^
'LazyData' is specified without a 'data' directory