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

> ### Name: cvFrobeniusLoss
> ### Title: Cross-Validation Function for Aggregated Frobenius Loss
> ### Aliases: cvFrobeniusLoss
> 
> ### ** Examples
> 
> library(MASS)
> library(origami)
origami v1.0.7: Generalized Framework for Cross-Validation
> library(rlang)
> 
> # generate 10x10 covariance matrix with unit variances and off-diagonal
> # elements equal to 0.5
> Sigma <- matrix(0.5, nrow = 10, ncol = 10) + diag(0.5, nrow = 10)
> 
> # sample 50 observations from multivariate normal with mean = 0, var = Sigma
> dat <- mvrnorm(n = 50, mu = rep(0, 10), Sigma = Sigma)
> 
> # generate a single fold using MC-cv
> resub <- make_folds(dat,
+   fold_fun = folds_vfold,
+   V = 2
+ )[[1]]
> cvFrobeniusLoss(
+   fold = resub,
+   dat = dat,
+   estimator_funs = rlang::quo(c(
+     linearShrinkEst, thresholdingEst, sampleCovEst
+   )),
+   estimator_params = list(
+     linearShrinkEst = list(alpha = c(0, 1)),
+     thresholdingEst = list(gamma = c(0, 1))
+   )
+ )
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Package which this enhances but not available for checking: 'RGtk2'
Documented arguments not in \usage in documentation object 'compute_stat':
  'K_0'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'robustbase'
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/cxhull.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES'
Documented arguments not in \usage in documentation object 'tree.filter':
  'nodeList'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'doMC'
Documented arguments not in \usage in documentation object 'default_params_doc':
  'islands' 'sort_clade_sizes'

Documented arguments not in \usage in documentation object 'integral_peak':
  '...'

Documented arguments not in \usage in documentation object 'sample_relaxed_rate':
  'relaxed_rate_pars'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'mm_run_reg':
  'all_params'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'DANN_distance':
  'x2'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'danstat-Ex.R' failed
The error most likely occurred in:

> ### Name: get_data
> ### Title: Get data for a particular table and variable selection
> ### Aliases: get_data
> 
> ### ** Examples
> 
> # Get data from table "folk1c" for selected values of variables "ieland" and "køn"
> # and all time periods available.
> 
> # The "ieland" variable is filtered for Denmark (id = 5000) and Bulgaria (id = 5128)
> # and the "køn" variable id filtered for Men (id = 1) and Women (id = 2).
> # The "tid" variable is unfiltered, i.e. selects all available time periods
> # See get_table_metadata(table_id = "folk1c", variables_only = TRUE) for variable codes and values.
> 
> variables <- list(list(code = "ieland", values = c(5100, 5128)),
+                   list(code = "køn", values = c(1,2)),
+                   list(code = "tid", values = NA))
> 
> data <- get_data("folk1c", variables)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [api.statbank.dk] Resolving timed out after 10008 milliseconds
Calls: get_data ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Introduction_to_danstat.Rmd' using rmarkdown

Quitting from lines 36-37 [unnamed-chunk-2] (Introduction_to_danstat.Rmd)
Error: processing vignette 'Introduction_to_danstat.Rmd' failed with diagnostics:
Timeout was reached: [api.statbank.dk] Resolving timed out after 10011 milliseconds
--- failed re-building 'Introduction_to_danstat.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Invalid package aliases in Rd file 'dap-package.Rd':
  'dap-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'plotDataExplorer.single':
  'obj'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
Error(s) in re-building vignettes:
--- re-building 'AdvancedTuning.Rmd' using rmarkdown
--- finished re-building 'AdvancedTuning.Rmd'

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

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

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

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

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

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

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

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

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

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

Quitting from lines 56-59 [unnamed-chunk-3] (PredictionExplanations.Rmd)
Error: processing vignette 'PredictionExplanations.Rmd' failed with diagnostics:
Timeout was reached: [] Resolving timed out after 10007 milliseconds
--- failed re-building 'PredictionExplanations.Rmd'

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'RDF.Rmd' using rmarkdown
--- finished re-building 'RDF.Rmd'

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

Quitting from lines 73-74 [unnamed-chunk-3] (dataset.Rmd)
Error: processing vignette 'dataset.Rmd' failed with diagnostics:
argument "subset" is missing, with no default
--- failed re-building 'dataset.Rmd'

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

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Documented arguments not in \usage in documentation object 'dotgetJSONValue':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Error(s) in re-building vignettes:
--- re-building 'A-introduction.Rmd' using rmarkdown
--- finished re-building 'A-introduction.Rmd'

--- re-building 'B-search.Rmd' using rmarkdown

Quitting from lines 21-24 [unnamed-chunk-1] (B-search.Rmd)
Error: processing vignette 'B-search.Rmd' failed with diagnostics:
Timeout was reached: [dataverse.harvard.edu] Resolving timed out after 10011 milliseconds
--- failed re-building 'B-search.Rmd'

--- re-building 'C-download.Rmd' using rmarkdown

Quitting from lines 46-50 [unnamed-chunk-3] (C-download.Rmd)
Error: processing vignette 'C-download.Rmd' failed with diagnostics:
Could not retrieve Dataset ID from persistent identifier!
--- failed re-building 'C-download.Rmd'

SUMMARY: processing the following files failed:
  'B-search.Rmd' 'C-download.Rmd'

Error: Vignette re-building failed.
Execution halted
Argument items with no description in Rd object 'zplot':
  'xlim' 'ylim'
Running examples in 'datelife-Ex.R' failed
The error most likely occurred in:

> ### Name: get_ott_children
> ### Title: Use this instead of 'rotl::tol_subtree()' when taxa are not in
> ###   synthesis tree and you still need to get all species or an induced
> ###   OpenTree subtree
> ### Aliases: get_ott_children
> 
> ### ** Examples
> 
> # An example with the dog genus:
> 
> # It is currently not possible to get an OpenTree subtree of a taxon that is
> #  missing from the OpenTree synthetic tree.
> # The dog genus is not monophyletic in the OpenTree synthetic tree, so in
> #  practice, it has no node to extract a subtree from.
> tnrs <- tnrs_match("Canis")
---> Runnning TNRS to match input names to reference taxonomy (OTT).
No internet connection or the Open Tree of Life's API is down.

Execution halted
Error(s) in re-building vignettes:
--- re-building 'Getting_started_with_datelife.Rmd' using rmarkdown
--- finished re-building 'Getting_started_with_datelife.Rmd'

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

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

Execution halted
--- re-building 'making_bold_trees.Rmd' using rmarkdown
--- finished re-building 'making_bold_trees.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'SASxport'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dblog'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'win_over':
  'parition'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES'
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'dbglm-inl':
  'dbglm.iteration'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'a_dcc_mat_est':
  'param'

Documented arguments not in \usage in documentation object 'dcc_mat_est':
  'param'

Documented arguments not in \usage in documentation object 'deco_mat_est':
  'param'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/DCLEAR.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'BRugs'
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in 'DDD-Ex.R' failed
The error most likely occurred in:

> ### Name: dd_KI_sim
> ### Title: Function to simulate a key innovation in macro-evolution with
> ###   the innovative clade decoupling from the diversity-dependent
> ###   diversification dynamics of the main clade
> ### Aliases: dd_KI_sim
> ### Keywords: models
> 
> ### ** Examples
> 
>  dd_KI_sim(c(0.2,0.1,20,0.1,0.05,30,4),10) 
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Missing or unexported object: 'Matrix::crossprod'
Running examples in 'ddml-Ex.R' failed
The error most likely occurred in:

> ### Name: crosspred
> ### Title: Cross-Predictions using Stacking.
> ### Aliases: crosspred
> 
> ### ** Examples
> 
> # Construct variables from the included Angrist & Evans (1998) data
> y = AE98[, "worked"]
> X = AE98[, c("morekids", "age","agefst","black","hisp","othrace","educ")]
> 
> # Compute cross-predictions using stacking with base learners ols and lasso.
> #     Two stacking approaches are simultaneously computed: Equally
> #     weighted (ensemble_type = "average") and MSPE-minimizing with weights
> #     in the unit simplex (ensemble_type = "nnls1"). Predictions for each
> #     learner are also calculated.
> crosspred_res <- crosspred(y, X,
+                            learners = list(list(fun = ols),
+                                            list(fun = mdl_glmnet)),
+                            ensemble_type = c("average",
+                                              "nnls1",
+                                              "singlebest"),
+                            compute_predictions_bylearner = TRUE,
+                            sample_folds = 2,
+                            cv_folds = 2,
+                            silent = TRUE)
Warning in MASS::ginv(X) : restarting interrupted promise evaluation
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'DDPNA-package':
  \details: '...o use the package, including the most important functions ~~'
Argument items with no description in Rd object 'DEP_Mod_net_plot':
  '\dots'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'getTriContextFraction':
  'trimer.counts.ref'

Documented arguments not in \usage in documentation object 'norm.it':
  'trimer.counts'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Running 'spelling.R' [0s]
  Running 'testthat.R' [161s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(deepdep)
  > 
  > test_check("deepdep")
  [ FAIL 1 | WARN 2 | SKIP 2 | PASS 45 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-plot.R:135:3', 'test-plot_downloads.R:8:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-deepdep.R:32:3'): obtaining Bioc dependencies returns objects of correct types ──
  Error in `value[[3L]](cond)`: Bioconductor version cannot be validated; no internet connection?  See
    #troubleshooting section in vignette
  Backtrace:
      ▆
   1. ├─vcr::use_cassette(...) at test-deepdep.R:32:2
   2. │ └─cassette$call_block(...)
   3. └─deepdep (local) deepdep_wrapped(...) at test-deepdep.R:33:4
   4.   └─base::tryCatch(...) at test-deepdep.R:3:2
   5.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   6.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7.         └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 2 | SKIP 2 | PASS 45 ]
  Error: Test failures
  Execution halted
Problems with news in 'NEWS.md':
No news entries found.
Missing or unexported object: 'Matrix::crossprod'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/deeptime.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/deeptrafo.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'degreenet-internal':
  'range' 'lims'
Objects in \usage without \alias in documentation object 'degreenet-internal':
  'bootstrapyule'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/DEGRE.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Running examples in 'demcon-Ex.R' failed
The error most likely occurred in:

> ### Name: get_cce
> ### Title: Retrieve Chronology of Constitutional Events Dataset
> ### Aliases: get_cce
> 
> ### ** Examples
> 
> 
> cce<-get_cce(del_file=TRUE, write_out = FALSE)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [comparativeconstitutionsproject.org] Resolving timed out after 10001 milliseconds
Calls: get_cce ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ccode-considerations.Rmd' using rmarkdown
--- finished re-building 'ccode-considerations.Rmd'

--- re-building 'clean-vdem.Rmd' using rmarkdown
--- finished re-building 'clean-vdem.Rmd'

--- re-building 'constitution-datasets.Rmd' using rmarkdown
--- finished re-building 'constitution-datasets.Rmd'

--- re-building 'constraint-indices.Rmd' using rmarkdown
--- finished re-building 'constraint-indices.Rmd'

--- re-building 'dem-datasets.Rmd' using rmarkdown

Quitting from lines 28-53 [sample-image] (dem-datasets.Rmd)
Error: processing vignette 'dem-datasets.Rmd' failed with diagnostics:
cannot read from connection
--- failed re-building 'dem-datasets.Rmd'

SUMMARY: processing the following file failed:
  'dem-datasets.Rmd'

Error: Vignette re-building failed.
Execution halted
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Documented arguments not in \usage in documentation object 'boot_f_cor':
  'fun'

Documented arguments not in \usage in documentation object 'boot_f_pcor':
  'fun'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Rd files without \alias:
  'densityClust-package.Rd'
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.N' '.Nmiss' '.Q1' '.Q3' '.factorN' '.factorNmiss' '.factorQ1'
  '.factorQ3' '.factormax' '.factormean' '.factormedian' '.factormin'
  '.factorsd' '.max' '.mean' '.median' '.min' '.sd'
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Packages which this enhances but not available for checking:
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installed size is  5.6Mb
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    data          1.8Mb
    htmlwidgets   3.6Mb
GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'encode_unit':
  'original'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Missing or unexported objects:
  'Matrix::crossprod' 'Matrix::tcrossprod'
Error(s) in re-building vignettes:
--- re-building 'Two-Stage-Difference-in-Differences.Rmd' using rmarkdown

Quitting from lines 144-153 [static] (Two-Stage-Difference-in-Differences.Rmd)
Error: processing vignette 'Two-Stage-Difference-in-Differences.Rmd' failed with diagnostics:
error in evaluating the argument 'a' in selecting a method for function 'solve': 'crossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'Two-Stage-Difference-in-Differences.Rmd'

SUMMARY: processing the following file failed:
  'Two-Stage-Difference-in-Differences.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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installed size is 10.8Mb
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Documented arguments not in \usage in documentation object 'Nortonbass_startvalgen':
  'param' 'startvalgen'

Documented arguments not in \usage in documentation object 'seqdiffusion':
  'w'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/digitalDLSorteR.Rcheck/00install.out' for details.
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Package suggested but not available for checking: 'rrelaxiv'
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checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
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installed size is 13.1Mb
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Documented arguments not in \usage in documentation object 'residuals_extrap':
  'n'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/DIscBIO.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'discreteMTP'
Unknown package 'discreteMTP' in Rd xrefs
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Invalid package aliases in Rd file 'RV.Rd':
  'RV-package'
'LazyData' is specified without a 'data' directory
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    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/dispRity.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
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Problems with news in 'NEWS.md':
No news entries found.
Documented arguments not in \usage in documentation object 'reshape_into_long':
  'pred_intvar'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'internals_for_distrEx':
  'namestoGather' 'namestoGatherNS'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'internal_mlehelpers_for_distrMod':
  'validity.check'

Objects in \usage without \alias in documentation object 'internals_for_distrMod':
  '.csimpsum'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Assignments in \usage in documentation object 'internalGenerics':
  x <- samplesize(object, value)

Documented arguments not in \usage in documentation object 'internals_for_distr':
  'DClass'
Objects in \usage without \alias in documentation object 'internals_for_distr':
  '.consolidategaps' '.List'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object 'diveMove-internal':
  '.diveMatches'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'BOLTSSIRR'
'LazyData' is specified without a 'data' directory
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installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
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Invalid package aliases in Rd file 'dmaiIntro.Rd':
  'dmaiIntro-package'
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Argument items with no description in Rd object 'dml_bagging':
  'y,x,d,data,sed'
Argument items with no description in Rd object 'dml_boosting':
  'y,x,d,data,sed'
Argument items with no description in Rd object 'dml_ensemble_lm':
  'y,x,d,data,sed'
Argument items with no description in Rd object 'dml_ensemble_rf':
  'y,x,d,data,sed'
Argument items with no description in Rd object 'dml_neural_network':
  'y,x,d,data,sed'
Argument items with no description in Rd object 'dml_random_forest':
  'y,x,d,data,sed'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
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Invalid package aliases in Rd file 'dnapath2-package.Rd':
  'dnapath2-package'
Auto-generated content requiring editing in Rd object 'dnapath2-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
Error(s) in re-building vignettes:
--- re-building 'introduction_to_dnapath.Rmd' using rmarkdown
--- finished re-building 'introduction_to_dnapath.Rmd'

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

Quitting from lines 126-135 [unnamed-chunk-8] (package_data.Rmd)
Error: processing vignette 'package_data.Rmd' failed with diagnostics:
Timeout was reached: [linkedomics.org] Resolving timed out after 10012 milliseconds
--- failed re-building 'package_data.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
Running examples in 'dnr-Ex.R' failed
The error most likely occurred in:

> ### Name: paramVertex
> ### Title: Parameter estimation for Vertex dynamics
> ### Aliases: paramVertex
> 
> ### ** Examples
> 
> nvertexstats <- 9
> maxLag = 3
> VertexLag = rep(1, maxLag)
> VertexLagMatrix <- matrix(0, maxLag, nvertexstats)
> VertexLagMatrix[, c(4, 7)] <- 1
> VertexLagMatrix[c(2,3),7] <- 0
> 
> getWeekend <- function(z){
+     weekends <- c("Saturday", "Sunday")
+     if(!network::is.network(z)){
+         if(is.na(z)) return(NA)
+     } else {
+          zDay <- get.network.attribute(z, attrname = "day")
+          out <- ifelse(zDay %in% weekends, 1, 0)
+          return(out)   
+     }
+ }
> 
> dayClass <- numeric(length(beach))
> for(i in seq_along(dayClass)) {
+     dayClass[i] <- getWeekend(beach[[i]])
+ }
> dayClass <- na.omit(dayClass)
> 
> 
> out <- paramVertex(InputNetwork = beach,
+                    maxLag = 3,
+                    VertexStatsvec = rep(1, nvertexstats),
+                    VertexModelGroup = "regular",
+                    VertexLag = rep(1, maxLag),
+                    VertexLagMatrix = VertexLagMatrix,
+                    dayClass = dayClass,
+                    EdgeModelTerms = NA,
+                    EdgeModelFormula = NA,
+                    EdgeGroup = NA,
+                    EdgeIntercept = c("edges"),
+                    EdgeNetparam = c("logSize"),
+                    EdgeExvar = NA,
+                    EdgeLag = c(1, 1, 0),
+                    paramout = TRUE)
Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'dnr_vignette.Rnw' using knitr
Warning: 'mode(width)' differs between new and previous
	 ==> NOT changing 'width'
Warning: 'mode(width)' differs between new and previous
	 ==> NOT changing 'width'
Warning: 'mode(width)' differs between new and previous
	 ==> NOT changing 'width'
Warning: 'mode(width)' differs between new and previous
	 ==> NOT changing 'width'
Warning: 'mode(width)' differs between new and previous
	 ==> NOT changing 'width'
Warning: 'mode(width)' differs between new and previous
	 ==> NOT changing 'width'

Quitting from lines 126-133 [beach-vertex-model-fit] (dnr_vignette.Rnw)
Error: processing vignette 'dnr_vignette.Rnw' failed with diagnostics:
objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
--- failed re-building 'dnr_vignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
S3 methods shown with full name in documentation object 'add.joint.mean.many':
  'all.cond.mean.PO' 'all.cond.mean2.PO'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Argument items with no description in Rd object 'derivType':
  'L' 'mu' 'eps'
Argument items with no description in Rd object 'getNewParams.SC':
  'n.fft'
Argument items with no description in Rd object 'graph.CTMC':
  '\dots'
Argument items with no description in Rd object 'num.deriv':
  '\dots'
Argument items with no description in Rd object 'power.coef.one':
  '\dots'
Documented arguments not in \usage in documentation object 'concDict':
  'text'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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    data   4.8Mb
    libs   1.1Mb
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'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'check_results':
  'error_on_failure' 'error_on_warning'

Documented arguments not in \usage in documentation object 'function_get_comments':
  'thresholds'

Documented arguments not in \usage in documentation object 'vignette_results_display':
  'vignette_results' 'error_on_failure'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.7Mb
GNU make is a SystemRequirements.
Objects in \usage without \alias in documentation object 'utilities':
  'generators.character'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/doolkit.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New features
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'OpenMPController'
'LazyData' is specified without a 'data' directory
Warning in url(sprintf("%s/%s", cran, path), open = "rb") :
  URL 'https://CRAN.R-project.org/src/contrib/Meta/aliases.rds': Timeout of 60 seconds was reached
Unknown package 'broomExtra' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
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Auto-generated content requiring editing in Rd object 'downscaledl-package':
  \references: '~~ Literature or other references for background information ~~'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/dowser.Rcheck/00install.out' for details.
Documented arguments not in \usage in documentation object 'show,dparserFunction-method':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
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Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'isolate_example':
  '...'

Documented arguments not in \usage in documentation object 'new_drake_deps':
  'restrict'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES'
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Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/DRomics.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/DR.SC.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'DrugSim2DR.Rmd' using rmarkdown

Quitting from lines 108-115 [unnamed-chunk-7] (DrugSim2DR.Rmd)
Error: processing vignette 'DrugSim2DR.Rmd' failed with diagnostics:
Please ensure smooth network connection
--- failed re-building 'DrugSim2DR.Rmd'

SUMMARY: processing the following file failed:
  'DrugSim2DR.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/DRviaSPCN.Rcheck/00install.out' for details.
installed size is  5.2Mb
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    appinformation   4.1Mb
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Documented arguments not in \usage in documentation object 'forecastCovCompiled':
  'obj' 'zero' 'trend' 'estimation.sample' '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'dsBaseClient'
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.6Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.0Mb
Objects in \usage without \alias in documentation object 'd.spls.norm1':
  'd.spls.norm2'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/DWLS.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R      3.3Mb
    data   8.3Mb
Package unavailable to check Rd xrefs: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'dynConfiR-package.Rd':
  'dynWEV-package'
Package suggested but not available for checking: 'lle'
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checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.0Mb
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    bin       3.1Mb
    extdata   1.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    20181118
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/easyDifferentialGeneCoexpression.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/easySdcTable.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Running examples in 'ecan-Ex.R' failed
The error most likely occurred in:

> ### Name: read_biss
> ### Title: Read data from BiSS (Biodiversity Investigation Support System)
> ###   to data frame.
> ### Aliases: read_biss
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

> # path <- "set file path"
> path <- "https://raw.githubusercontent.com/matutosi/biodiv/main/man/example.json"
> read_biss(path)
Warning in open.connection(con, "rb") :
  URL 'https://raw.githubusercontent.com/matutosi/biodiv/main/man/example.json': status was 'Failure when receiving data from the peer'
Error in open.connection(con, "rb") : 
  cannot open the connection to 'https://raw.githubusercontent.com/matutosi/biodiv/main/man/example.json'
Calls: read_biss ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
Package suggested but not available for checking: 'INLA'
Running examples in 'ecb-Ex.R' failed
The error most likely occurred in:

> ### Name: get_data
> ### Title: Retrieve data from the ECB Statistical Data Warehouse API
> ### Aliases: get_data
> 
> ### ** Examples
> 
> # Get monthly data on annualized euro area headline HICP
> hicp <- get_data("ICP.M.U2.N.000000.4.ANR")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [sdw-wsrest.ecb.europa.eu] Send failure: Connection was reset
Calls: get_data ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'e.cluster.decision':
  'reg_data' 'log.lambda'
Argument items with no description in Rd object 'e.cluster.dendrogram':
  'echelon.obj' 'n.sim' 'cluster.legend.pos' 'cluster_reg' 'p_rank'
  'para'
Argument items with no description in Rd object 'e.cluster.map':
  'x' 'c_separates' 'locs' 'coo' 'rin' 'p_rank' 'cluster_reg' 'n.sim'
  'cluster.type'
Argument items with no description in Rd object 'e.dendrogram':
  'peaks' 'locs' 'x' 'separates' 'c_separates' 'number' 'parents'
  'pare_locs' 'progeny' 'symbols' 'col.symbols' 'cex.symbols' 'lwd'
  'col' 'ens' 'adj.ens' 'col.ens' 'cex.ens' 'limb'
Argument items with no description in Rd object 'e.dendrogram.axis':
  'main' 'ylab' 'yaxes' 'ylim' 'xaxes' 'xdper' 'dmai' 'peaks' 'x'
Argument items with no description in Rd object 'e.main':
  'x' 'rin' 'T'
Argument items with no description in Rd object 'e.monte.bin':
  'rin' 'cas' 'pop' 'n.sim' 'K' 'cluster.type'
Argument items with no description in Rd object 'e.monte.poi':
  'rin' 'cas' 'pop' 'ex' 'n.sim' 'K' 'cluster.type'
Argument items with no description in Rd object 'e.profile':
  'peaks' 'parents' 'separates'
Argument items with no description in Rd object 'e.scan':
  'x' 'locs' 'peaks' 'c_separates' 'parents' 'K'
Argument items with no description in Rd object 'e.scan.pop':
  'x' 'locs' 'peaks' 'c_separates' 'parents' 'K' 'pop'
Argument items with no description in Rd object 'nlimb':
  'x' 'k2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
+   observation = observation, 
+   observation_ancillary = observation_ancillary)
Writing tables to file:
  observation
  observation_ancillary
> 
> dir(mypath)
[1] "observation.csv"           "observation_ancillary.csv"
> 
> # Clean up
> unlink(mypath, recursive = TRUE)
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  12.08 0.81 12.91 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/economiccomplexity.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::tcrossprod'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'fcf.env':
  'vars'

Documented arguments not in \usage in documentation object 'getlevels':
  'editarray'

Documented arguments not in \usage in documentation object 'parseCatEdit':
  'e'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'introducing-educationdata.Rmd' using rmarkdown

Quitting from lines 55-64 [usage-02] (introducing-educationdata.Rmd)
Error: processing vignette 'introducing-educationdata.Rmd' failed with diagnostics:
Timeout was reached: [educationdata.urban.org] Resolving timed out after 10013 milliseconds
--- failed re-building 'introducing-educationdata.Rmd'

SUMMARY: processing the following file failed:
  'introducing-educationdata.Rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/eeptools.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'eggCountsExtra'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object 'rotate_to_equilibrium':
  'xy_may'

Documented arguments not in \usage in documentation object 'wide.dyads.to.edgelist':
  'fist.var'

Documented arguments not in \usage in documentation object 'wide.to.long':
  'last.col' 'ego.vars'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Invalid package aliases in Rd file 'HOF-package.Rd':
  'HOF-package'
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
Error(s) in re-building vignettes:
--- re-building 'EHRtemporalVariability.Rmd' using rmarkdown

Quitting from lines 98-100 [EHRtemporalVariabilityObj1] (EHRtemporalVariability.Rmd)
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
cannot open the connection to 'https://github.com/hms-dbmi/EHRtemporalVariability-DataExamples/raw/master/variabilityDemoNHDS.RData'
--- failed re-building 'EHRtemporalVariability.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'colBoxplot4':
  'id'

Documented arguments not in \usage in documentation object 'elaborator_server':
  'id'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/elastes.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'bbox_to_sp':
  'bbx'

Documented arguments not in \usage in documentation object 'get_aws_terrain':
  'bbx'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/EMAS.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found export directive that requires package 'methods':
  'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  'enc-package.Rd'
'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: 'RStoolbox'
Documented arguments not in \usage in documentation object 'div_plot':
  'plot_cols'

Documented arguments not in \usage in documentation object 'seq_plot':
  'plot_cols'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Auto-generated content requiring editing in Rd object 'EnviroPRA-package':
  \details: '...o use the package, including the most important functions ~~'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/EnvNJ.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
'LazyData' is specified without a 'data' directory
Found export directives that require package 'methods':
  'exportClasses' 'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'epidict'
Documented arguments not in \usage in documentation object 'dots_to_charlist':
  'call' '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.0Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    help   1.5Mb
    libs   7.6Mb
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/epiomics.Rcheck/00install.out' for details.
S3 methods shown with full name in documentation object 'addDrug.Lexis':
  'addDrug.Lexis'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [23s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(EPLSIM)
  > 
  > test_check('EPLSIM')
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test.plsi.lr.v1.R:17:3'): Output of plsi.lr.v1 ──────────────────────
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─EPLSIM::plsi.lr.v1(...) at test.plsi.lr.v1.R:17:2
   2. └─base::loadNamespace(x)
   3.   ├─base::namespaceImportFrom(...)
   4.   │ └─base::asNamespace(ns)
   5.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   6.     └─base::namespaceImportFrom(...)
   7.       └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'equateMultiple-package.Rd':
  'EquateMultiple-package'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'subnetwork_templates':
  'nams.vattr'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'call.ErgmTerm':
  'A'

Objects in \usage without \alias in documentation object 'ergm-defunct':
  'sociality'

Documented arguments not in \usage in documentation object 'ergm-deprecated':
  'fname' 'varnames' 'vartypes' 'defaultvalues' 'required'
  'nw.bipartiteflag' 'requirement' 'extramessage' 'nw.directedflag' 'm'
  'response' 'new' 'from.new' 'model' 'proposal' 'eta0' 'control'
  'verbose' 'update.nws' 'Clist' 'prev.run' 'burnin' 'samplesize'
  'interval' 'maxedges' 'attrname' 'label' 'coord' 'jitter' 'thresh'
  'usearrows' 'mode' 'displayisolates' 'interactive' 'xlab' 'ylab'
  'xlim' 'ylim' 'pad' 'label.pad' 'displaylabels' 'boxed.labels'
  'label.pos' 'label.bg' 'vertex.sides' 'vertex.rot' 'arrowhead.cex'
  'label.cex' 'loop.cex' 'vertex.cex' 'edge.col' 'label.col'
  'vertex.col' 'label.border' 'vertex.border' 'edge.lty' 'label.lty'
  'vertex.lty' 'edge.lwd' 'label.lwd' 'edge.len' 'edge.curve'
  'edge.steps' 'loop.steps' 'object.scale' 'uselen' 'usecurve'
  'suppress.axes' 'vertices.last' 'layout.par' 'cex.main' 'cex.sub'
  'seed' 'latent.control' 'colornames' 'latent' 'preserve.eattr'

Documented arguments not in \usage in documentation object 'ergm_state':
  'nw'

Documented arguments not in \usage in documentation object 'nodal_attributes-API':
  'l'

Documented arguments not in \usage in documentation object 'summary.ergm_model':
  'response'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'summary.error_interval':
  'summary.error_interval'

S3 methods shown with full name in documentation object 'summary.measure':
  'summary.measure'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'esaBcv_package.Rd':
  'esaBcv_package-package'
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Bootstrap_implementation.Rmd' using rmarkdown
--- finished re-building 'Bootstrap_implementation.Rmd'

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

Quitting from lines 30-41 [unnamed-chunk-1] (Examples.Rmd)
Error: processing vignette 'Examples.Rmd' failed with diagnostics:
Timeout was reached: [raw.githubusercontent.com] Failed to connect to raw.githubusercontent.com port 443 after 9391 ms: Timed out
--- failed re-building 'Examples.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'ETAS-internal':
  'Smooth.catalog'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    libs      1.0Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
+   valid_year_month(years = mets_ws, months = 10,
+     begin = clinton$start, end = clinton$end)
+ }
Loading required package: ggplot2
# A tibble: 1 × 4
   year month month_begin month_end 
  <dbl> <dbl> <date>      <date>    
1  2000    10 2000-10-01  2000-10-31
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:ggplot2'

> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.91 0.38 12.49 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Documented arguments not in \usage in documentation object 'poly_clip':
  'x' 'y'

Documented arguments not in \usage in documentation object 'setup_gpar':
  'x'

Documented arguments not in \usage in documentation object 'setup_grobs':
  'centers'

Documented arguments not in \usage in documentation object 'update_list':
  'x' 'val'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(europepmc)
  > 
  > test_check("europepmc")
  [ FAIL 1 | WARN 0 | SKIP 20 | PASS 0 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • On CRAN (20): 'test_annotations_by_id.r:4:3', 'test_epmc_citations.r:4:3',
    'test_epmc_db.r:4:3', 'test_epmc_db_count.r:4:3', 'test_epmc_details.r:4:3',
    'test_epmc_ftxt.r:4:3', 'test_epmc_ftxt_book.r:4:3', 'test_epmc_hits.r:4:3',
    'test_epmc_hits_trend.R:4:3', 'test_epmc_hits_trend.R:30:3',
    'test_epmc_lablinks.r:4:3', 'test_epmc_lablinks_count.r:4:3',
    'test_epmc_profile.r:4:3', 'test_epmc_profile.r:22:3',
    'test_epmc_refs.r:4:3', 'test_epmc_search.r:4:3', 'test_epmc_search.r:54:3',
    'test_epmc_search_by_doi.r:4:3', 'test_epmc_tm.r:4:3',
    'test_epmc_tm_count.r:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_epmc_hits_trend.R:39:3'): epmc_hits_trend synonym search works correctly ──
  <http_404/http_400/http_error/error/condition>
  Error in `rebi_GET(path = paste0(rest_path(), "/profile"), query = args)`: Not Found (HTTP 404).
  Backtrace:
      ▆
   1. └─europepmc::epmc_hits_trend("malaria", period = 2012:2016, synonym = FALSE) at test_epmc_hits_trend.R:39:2
   2.   └─base::lapply(...)
   3.     └─europepmc (local) FUN(X[[i]], ...)
   4.       └─europepmc::epmc_profile(queryforall, synonym)
   5.         └─europepmc:::rebi_GET(...)
   6.           └─httr::stop_for_status(req)
  
  [ FAIL 1 | WARN 0 | SKIP 20 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Documented arguments not in \usage in documentation object 'doHttrRequest':
  'params' 'customConfig'

Documented arguments not in \usage in documentation object 'errorMessage':
  'test_me'

Documented arguments not in \usage in documentation object 'isError':
  'test_me'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/evobiR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/evolqg.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
Running examples in 'EvoPhylo-Ex.R' failed
The error most likely occurred in:

> ### Name: plot_treerates_sgn
> ### Title: Plot Bayesian evolutionary tree with rate thresholds for
> ###   selection mode
> ### Aliases: plot_treerates_sgn
> 
> ### ** Examples
> 
> # See vignette("rates-selection") for how to use this
> # function as part of an analysis pipeline
> 
> ## MrBayes example
> # Load example tree and posterior
> data("tree3p")
> data("posterior3p")
> 
> plot_treerates_sgn(
+   type = "MrBayes",
+   tree3p, posterior3p,          #MrBayes tree file with data for all partitions
+   trans = "none",
+   summary = "mean",             #MrBayes specific argument
+   drop.dummyextant = TRUE,      #MrBayes specific argument
+   clock = 1,                           #Show rates for clock partition 1
+   threshold = c("1 SD", "3 SD"),       #sets background rate threshold for selection mode
+   branch_size = 1.5, tip_size = 3,                          #sets size for tree elements
+   xlim = c(-450, -260), nbreaks = 8, geo_size = list(3, 3)) #sets limits and breaks for geoscale
ℹ invalid tbl_tree object. Missing column: parent.
ℹ invalid tbl_tree object. Missing column: parent.
ℹ invalid tbl_tree object. Missing column: parent.
ℹ invalid tbl_tree object. Missing column: parent.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'char-part.Rmd' using rmarkdown

Quitting from lines 29-30 [unnamed-chunk-2] (char-part.Rmd)
Error: processing vignette 'char-part.Rmd' failed with diagnostics:
The package "deeptime" (>= 0.2.0) is required.
--- failed re-building 'char-part.Rmd'

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

--- re-building 'fbd-params.Rmd' using rmarkdown

Quitting from lines 28-29 [unnamed-chunk-2] (fbd-params.Rmd)
Error: processing vignette 'fbd-params.Rmd' failed with diagnostics:
The package "deeptime" (>= 0.2.0) is required.
--- failed re-building 'fbd-params.Rmd'

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

Quitting from lines 35-36 [unnamed-chunk-2] (offset_handling.Rmd)
Error: processing vignette 'offset_handling.Rmd' failed with diagnostics:
The package "deeptime" (>= 0.2.0) is required.
--- failed re-building 'offset_handling.Rmd'

--- re-building 'rates-selection_BEAST2.Rmd' using rmarkdown

Quitting from lines 28-29 [unnamed-chunk-2] (rates-selection_BEAST2.Rmd)
Error: processing vignette 'rates-selection_BEAST2.Rmd' failed with diagnostics:
The package "deeptime" (>= 0.2.0) is required.
--- failed re-building 'rates-selection_BEAST2.Rmd'

--- re-building 'rates-selection_MrBayes.Rmd' using rmarkdown

Quitting from lines 28-29 [unnamed-chunk-2] (rates-selection_MrBayes.Rmd)
Error: processing vignette 'rates-selection_MrBayes.Rmd' failed with diagnostics:
The package "deeptime" (>= 0.2.0) is required.
--- failed re-building 'rates-selection_MrBayes.Rmd'

SUMMARY: processing the following files failed:
  'char-part.Rmd' 'fbd-params.Rmd' 'offset_handling.Rmd'
  'rates-selection_BEAST2.Rmd' 'rates-selection_MrBayes.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'borrOrderingInternal':
  'n.cntrl'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: 'ExactData'
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./RUtils.h:19:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  RUtils.c:144:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/excel.link.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
'LazyData' is specified without a 'data' directory
Unknown package 'iptools' in Rd xrefs
Package suggested but not available for checking: 'INLA'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    exiftool  14.1Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ExomeDepth.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cec2013'
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
Argument items with no description in Rd object 'plot.expectreg':
  '\dots'
Argument items with no description in Rd object 'update.expectreg':
  '\dots'
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(explor)
  > 
  > test_check("explor")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 102 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_prepare_results_textmodel_ca.R:8:1'): (code run outside of `test_that()`) ──
  Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─quanteda.textmodels::textmodel_ca(dfmat, nd = 7) at test_prepare_results_textmodel_ca.R:8:0
   2. └─quanteda.textmodels:::textmodel_ca.dfm(dfmat, nd = 7)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 102 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
Argument items with no description in Rd object 'fbvpot':
  'cutoff'
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Documented arguments not in \usage in documentation object 'getQQLimit':
  'N' 'rho'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'exuberdata'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Package suggested but not available for checking: 'doMC'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::tcrossprod'
Running examples in 'ez-Ex.R' failed
The error most likely occurred in:

> ### Name: ezPredict
> ### Title: Compute predicted values from the fixed effects of a mixed
> ###   effects model
> ### Aliases: ezPredict
> 
> ### ** Examples
> 
> library(lme4)
Loading required package: Matrix
> 
> #Read in the ANT data (see ?ANT).
> data(ANT)
> head(ANT)
  subnum     group block trial     cue     flank location direction       rt
1      1 Treatment     1     1    None   Neutral       up      left 398.6773
2      1 Treatment     1     2  Center   Neutral       up      left 389.1822
3      1 Treatment     1     3  Double   Neutral       up      left 333.2186
4      1 Treatment     1     4 Spatial   Neutral       up      left 419.7640
5      1 Treatment     1     5    None Congruent       up      left 446.4754
6      1 Treatment     1     6  Center Congruent       up      left 338.9766
  error
1     0
2     0
3     0
4     0
5     0
6     0
> 
> #fit a mixed effects model to the rt data
> rt_fit = lmer(
+     formula = rt ~ cue*flank*group + (1|subnum)
+     , data = ANT[ANT$error==0,]
+ )
boundary (singular) fit: see help('isSingular')
> 
> #obtain the predictions from the model
> rt_preds = ezPredict(
+     fit = rt_fit
+ )
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'complete.log.likelihood_Sj':
  'z'
Auto-generated content requiring editing in Rd object 'getStuffForDIC':
  \details: 'If necessary, more details than the description above'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    minor changes
Package suggested but not available for checking: 'hier.part'
Unknown package 'hier.part' in Rd xrefs
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object 'procrustes_switching':
  \details: 'If necessary, more details than the description above.'
Auto-generated content requiring editing in Rd object 'rsp_exact':
  \details: 'If necessary, more details than the description above.'
Auto-generated content requiring editing in Rd object 'rsp_full_sa':
  \details: 'If necessary, more details than the description above.'
Auto-generated content requiring editing in Rd object 'rsp_partial_sa':
  \details: 'If necessary, more details than the description above.'
Auto-generated content requiring editing in Rd object 'weighted_procrustes_switching':
  \details: 'If necessary, more details than the description above.'
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'Factoshiny-package':
  \references: '~~ Literature or other references for background information ~~'
  \seealso: '~~ Optional links to other man pages, e.g. ~~'
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.0Mb
    help   1.2Mb
Documented arguments not in \usage in documentation object '.get_default_sign_size':
  'outcome_type'

Documented arguments not in \usage in documentation object '.get_iteration_data':
  'file_dir'

Documented arguments not in \usage in documentation object 'extract_model_vimp':
  'feature_similarity_table'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'check_cache':
  'data' 'reset'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/faoutlier.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'kkk':
  'Vector'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'Get_C_R_K_Q':
  'have_noise'

Documented arguments not in \usage in documentation object 'Sample_KF_post':
  'C0'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     1.3Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'coxKM'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Rd files without \alias:
  'FastPCS-package.Rd'
Specified C++11: please drop specification unless essential
checkRd: (-1) Scent.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) Traffic.Rd:44: Escaped LaTeX specials: \&
Invalid package aliases in Rd file 'fastR-package.Rd':
  'fastR-package'
Specified C++11: please drop specification unless essential
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Invalid package aliases in Rd file 'FastRCS-package.Rd':
  'FastPCS-package'
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
Found the following significant warnings:
  Rconnection.cc:282:52: warning: format '%p' expects argument of type 'void*', but argument 3 has type 'Rexp*' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    Rcgi      3.0Mb
    cgi-bin   2.8Mb
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Undefined global functions or variables:
  init run
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'bin':
  'Integer'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'NNLM'
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
    libs   1.6Mb
Unexported object imported by a ':::' call: 'fdapace:::interp2lin'
  See the note in ?`:::` about the use of this operator.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
GNU make is a SystemRequirements.
Argument items with no description in Rd object 'getbasispenalty':
  'Lfdobj'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'xtable.fdt':
  'xtable.fdt' 'xtable.fdt.multiple' 'xtable.fdt_cat.multiple'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'url_base':
  'url'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 
> transaction_counter(leagueId = "42654852")
# A tibble: 4 × 14
  seasonId scoringPeriodId teamId abbrev waiverRank acquisitionBudgetSpent
     <int>           <int>  <int> <fct>       <int>                  <int>
1     2022              19      1 AUS             1                      0
2     2022              19      2 BOS             3                      0
3     2022              19      3 CHI             4                      0
4     2022              19      4 DEN             2                      0
# ℹ 8 more variables: acquisitions <int>, drops <int>, misc <int>,
#   moveToActive <int>, moveToIR <int>, paid <dbl>, teamCharges <dbl>,
#   trades <int>
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  8.39 0.28 25.54 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Documented arguments not in \usage in documentation object 'linregEst':
  'rank_lim' 'Umodel'

Documented arguments not in \usage in documentation object 'm2c':
  'CC'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'checkStream':
  'skipChecks'

Documented arguments not in \usage in documentation object 'cpp_detectCUSUMMeanSinglePrechange':
  'BL'

Documented arguments not in \usage in documentation object 'cpp_detectEWMAMeanSinglePrechange':
  'BL'

Documented arguments not in \usage in documentation object 'makeStreamMeanChangeR':
  'x'

Documented arguments not in \usage in documentation object 'update_Omega':
  'm_new'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'recode_subquad':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running 'spelling.R' [0s]
  Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(fgeo.tool)
  
  Attaching package: 'fgeo.tool'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("fgeo.tool")
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    extdata   2.8Mb
    libs      1.2Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'MicrobeDS'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    2.2Mb
    help   1.1Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R         4.5Mb
    doc       2.1Mb
    extdata   2.1Mb
Found the following significant warnings:
  filelock-windows.c:17:5: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/filelock.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'filename.Rd':
  'filename-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Documented arguments not in \usage in documentation object 'print.data.frame.ff':
  '.data'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/FindIt.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'diveRsity'
Unknown package 'diveRsity' in Rd xrefs
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Missing or unexported object: 'Matrix::tcrossprod'
Running examples in 'FinNet-Ex.R' failed
The error most likely occurred in:

> ### Name: FF.binary.management
> ### Title: Create a binary firm-firm (FF) matrix for board interlocks
> ### Aliases: FF.binary.management
> 
> ### ** Examples
> 
> 
> # Create the binary FF matrix of Berkshire Hathaway's holdings by boards interlock
> data('firms_BKB')
> FF <- FF.binary.management(firms_BKB)
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    lib    3.0Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Documented arguments not in \usage in documentation object 'plot_data_type':
  'client_id' 'client_secret' 'refresh_token'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fivethirtyeightdata'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.6Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) cclust.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) randIndex.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:28: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'FPCEnv'
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/flexrsurv.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    9.1Mb
    libs   1.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Invalid package aliases in Rd file 'FLPS-package.Rd':
  'FLPS-package'
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'RD_impData':
  'cutoff'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'hl.factor.number':
  'w'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/footBayes.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'FossilSim-Ex.R' failed
The error most likely occurred in:

> ### Name: FossilSim
> ### Title: FossilSim: A package for simulating and plotting fossil and
> ###   taxonomy data
> ### Aliases: FossilSim
> 
> ### ** Examples
> 
> # simulate a tree using TreeSim conditioned on tip number
> t = TreeSim::sim.bd.taxa(n = 10, numbsim = 1, lambda = 1, mu = 0.2)[[1]]
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SAtree.Rmd' using rmarkdown
--- finished re-building 'SAtree.Rmd'

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

Quitting from lines 75-91 [unnamed-chunk-2] (fossils.Rmd)
Error: processing vignette 'fossils.Rmd' failed with diagnostics:
object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'fossils.Rmd'

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

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

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

Quitting from lines 28-31 [unnamed-chunk-1] (simfbd.Rmd)
Error: processing vignette 'simfbd.Rmd' failed with diagnostics:
object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'simfbd.Rmd'

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

Quitting from lines 106-122 [unnamed-chunk-3] (taxonomy.Rmd)
Error: processing vignette 'taxonomy.Rmd' failed with diagnostics:
object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'taxonomy.Rmd'

SUMMARY: processing the following files failed:
  'fossils.Rmd' 'simfbd.Rmd' 'taxonomy.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RandomFields'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   3.4Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
Running 'testthat.R' [29s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > test_check("freegroup")
  Loading required package: freegroup
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  Loading required package: magic
  Loading required package: abind
  Loading required package: plyr
  
  Attaching package: 'freegroup'
  
  The following object is masked from 'package:plyr':
  
      id
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1006 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_aab.R:19:9'): Test suite aab.R ───────────────────────────────
  all(X == X %>% autosub("a", S) %>% autosub("a", -S)) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  Backtrace:
      ▆
   1. └─freegroup (local) autosub_checker(X = rfree(n, r), S = discard(rfree(1, r), "a")) at test_aab.R:19:8
   2.   └─testthat::expect_true(...) at test_aab.R:7:4
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1006 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'assert.surface':
  'surf'

Documented arguments not in \usage in documentation object 'check.dtype.for.data':
  'silent'

Documented arguments not in \usage in documentation object 'fread3':
  'filehandle:'

Documented arguments not in \usage in documentation object 'fwrite3':
  'filehandle:' 'data:'

Documented arguments not in \usage in documentation object 'polygon.soup.to.indexed.mesh':
  'face_vertex_coords'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'freqdom.transpose':
  'S'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
checkRd: (-1) NEWS.Rd:234: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:257: Escaped LaTeX specials: \_ \_
checkRd: (-1) NEWS.Rd:258: Escaped LaTeX specials: \_ \_
checkRd: (-1) NEWS.Rd:259: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:262: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:265: Escaped LaTeX specials: \_
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.7Mb
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'draw.colorbar':
  'coloredmesh'

Documented arguments not in \usage in documentation object 'extend_neighbors':
  'min_dotp_threshold'

Documented arguments not in \usage in documentation object 'surf.sphere.spatialfilter':
  'gaussian_weight'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Argument items with no description in Rd object 'fsdam':
  'verbose' 'which'
Argument items with no description in Rd object 'plot.classes':
  '\dots'
Argument items with no description in Rd object 'predict.fsim':
  '\dots'
Argument items with no description in Rd object 'predict.lm':
  '\dots'
Argument items with no description in Rd object 'predict.sfpl':
  '\dots'
Argument items with no description in Rd object 'predict.sfplsim.FASSMR':
  '\dots'
Argument items with no description in Rd object 'print.summary.mfplsim':
  '\dots'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'imp_small_gaps_WMA':
  'Data' 'univariate'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Objects in \usage without \alias in documentation object 'funData-constructor':
  'funData'

Objects in \usage without \alias in documentation object 'irregFunData-constructor':
  'irregFunData'

Objects in \usage without \alias in documentation object 'multiFunData-constructor':
  'multiFunData'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'plot.funData':
  'plot.funData'

S3 methods shown with full name in documentation object 'plot.irregFunData':
  'plot.irregFunData'

S3 methods shown with full name in documentation object 'plot.multiFunData':
  'plot.multiFunData'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/funmediation.Rcheck/00install.out' for details.
Documented arguments not in \usage in documentation object 'build_limits_lookup':
  'min_preds' 'max_preds' 'min_ratio' 'max_ratio' 'draw_unadjusted'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/funspace.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/funtimes.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'loggedOutput':
  'future'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'mandelbrot':
  'Z' 'xmid' 'ymid' 'side' 'resolution' 'maxIter' 'tau'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   4.2Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/g3viz.Rcheck/00install.out' for details.
Invalid package aliases in Rd file 'GAabbreviate-internal.Rd':
  'GAabbreviation-package'
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ##D search_fields("cl22") |> 
> ##D   show_values()
> ##D 
> ##D # Search for any values in field 'cl22' that match 'tas'
> ##D search_fields("cl22") |> 
> ##D   search_values("tas")
> ##D 
> ##D # See items within species list "dr19257"
> ##D search_lists("dr19257") |> 
> ##D   show_values()
> ## End(Not run)
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  2.8 0.24 3.04 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Documented arguments not in \usage in documentation object 'splitQTL_comment':
  'output_qtls'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
Invalid package aliases in Rd file 'gamlss.mx.package.Rd':
  'gamlss.mix-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
Documented arguments not in \usage in documentation object 'as.gapdata':
  'labels_df'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Specified C++14: please drop specification unless essential
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    doc   44.3Mb
    libs   1.2Mb
':::' call which should be '::': 'graphics:::grid'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.8Mb
Documented arguments not in \usage in documentation object 'lrr_plot':
  'plot_cols'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/GaussSuppression.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'tools:::.Rd_get_argument_names' 'tools:::RdTags' 'tools:::fetchRdDB'
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Documented arguments not in \usage in documentation object 'align_peaks':
  'gc_peak_df'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'paleofire'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 98.3Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     2.9Mb
    libs    83.8Mb
    proj     8.3Mb
installed size is 94.5Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      2.9Mb
    libs     82.1Mb
    proj      8.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    perl   3.9Mb
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object 'geepack-internal':
  'genZcor'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/geiger.Rcheck/00install.out' for details.
Auto-generated content requiring editing in Rd object 'gemlog-package':
  \details: '...the package, including the most important ~~ ~~ functions ~~'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.2Mb
    libs      1.1Mb
checkRd: (-1) plot_summary.Rd:14: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Running examples in 'genBaRcode-Ex.R' failed
The error most likely occurred in:

> ### Name: plotClusterGgTree
> ### Title: Plotting a Cluster ggTree
> ### Aliases: plotClusterGgTree
> 
> ### ** Examples
> 
> data(BC_dat)
> plotClusterGgTree(BC_dat, tree_est = "UPGMA", type = "circular")
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(genBaRcode)
  > 
  > test_check("genBaRcode")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 21 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_raw_data_functions.R:44:3'): processingRawData - extractBarcodes ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_raw_data_functions.R:44:2
   2.   ├─base::namespaceImport(...)
   3.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   4.     ├─base::namespaceImport(...)
   5.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   6.       ├─base::namespaceImport(...)
   7.       └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   8.         └─base::namespaceImportFrom(...)
   9.           └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_raw_data_functions.R:121:3'): processingRawData - fixBorderlineBCs and extractWobble ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_raw_data_functions.R:121:2
   2.   ├─base::namespaceImport(...)
   3.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   4.     ├─base::namespaceImport(...)
   5.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   6.       ├─base::namespaceImport(...)
   7.       └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   8.         └─base::namespaceImportFrom(...)
   9.           └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 21 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'genBaRcode_GUI_Vignette.Rmd' using rmarkdown
--- finished re-building 'genBaRcode_GUI_Vignette.Rmd'

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

Quitting from lines 155-176 [unnamed-chunk-4] (genBaRcode_Vignette.Rmd)
Error: processing vignette 'genBaRcode_Vignette.Rmd' failed with diagnostics:
objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
--- failed re-building 'genBaRcode_Vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Invalid package aliases in Rd file 'GenBinom-package.Rd':
  'GenbinomApps-package'
Package suggested but not available for checking: 'genderdata'
Documented arguments not in \usage in documentation object 'CirDisp':
  'x'

Documented arguments not in \usage in documentation object 'CirKurt':
  'x' 'na.rm'

Documented arguments not in \usage in documentation object 'CirSD':
  'x'

Documented arguments not in \usage in documentation object 'CirSkew':
  'x'

Documented arguments not in \usage in documentation object 'CirVar':
  'x'

Documented arguments not in \usage in documentation object 'MeanDir':
  'x'

Documented arguments not in \usage in documentation object 'impact':
  'na.rm'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'expand':
  'x'

Documented arguments not in \usage in documentation object '%bq%':
  'x'

Documented arguments not in \usage in documentation object '%bt%':
  'x'

Documented arguments not in \usage in documentation object 'stftcalc':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/geneHapR.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object 'generalizedwendland-internal':
  'numint.abstol (default: 1e-3)' 'numint.reltol (default: 1e-3)'
  'numint.qag_key (default: 0)' 'numint.subintervals (default: 0)'
  'interp.method (default: 'none')' 'interp.num_support (default: 0)'
  'cov.reparameterize (default: TRUE)' 'cov.eps (default:
  .Machine$double.eps^0.5)' 'cov.d_value (default: 2)'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'GenlibR-package.Rd':
  'GenlibR-package'
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'bin.levels':
  'variable'

Documented arguments not in \usage in documentation object 'info.mox':
  'y:'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   3.0Mb
    libs      1.4Mb
Documented arguments not in \usage in documentation object 'adj_spconsist_arr_window_globstd':
  'a'

Documented arguments not in \usage in documentation object 'elsa_fuzzy_vector':
  'nbslitw'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'variables_query':
  'variables'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'geomarocdata'
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R         9.6Mb
    extdata   2.5Mb
    help      2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/GeoModels.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/geomod.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ###   wk_writer.geos_geometry
> 
> ### ** Examples
> 
> library(wk)
> wk_handle(as_geos_geometry("POINT (1 2)"), wk::wkt_writer())
<wk_wkt[1]>
[1] POINT (1 2)
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:wk'

> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.23 0.08 1.31 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) getopt.Rd:60: Escaped LaTeX specials: \#
Package suggested but not available for checking: 'argon2'
Package suggested but not available for checking: 'RGtk2'
checkRd: (-1) estGF.Rd:106: Escaped LaTeX specials: \&
checkRd: (-1) estGF.Rd:107: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("gfpop")
  Loading required package: gfpop
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 40 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-sn.R:3:1'): (code run outside of `test_that()`) ────────────────
  <install_error/error/condition>
  Error: Failed to install 'gfpop.data' from GitHub:
    Timeout was reached: [api.github.com] Connection timeout after 10008 ms
  Backtrace:
      ▆
   1. └─devtools::install_github("vrunge/gfpop.data") at test-sn.R:3:0
   2.   ├─pkgbuild::with_build_tools(...)
   3.   │ └─pkgbuild:::withr_with_path(rtools_path(), code)
   4.   │   └─base::force(code)
   5.   └─remotes:::install_remotes(...)
   6.     └─base::tryCatch(...)
   7.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   8.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 40 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'attract_by_distance':
  'prop_start' 'prop_end'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ggcoverage.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'labels.rpart':
  'pretty:'

Documented arguments not in \usage in documentation object 'rpart_labels':
  'model' '...'

Documented arguments not in \usage in documentation object 'rpart_segments':
  'model'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'interpolateDataFrame':
  'A'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': 'scales:::censor'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'productplots:::bound'
  See the note in ?`:::` about the use of this operator.
Argument items with no description in Rd object 'isADMG':
  'amat'
Argument items with no description in Rd object 'isAG':
  'amat'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'package-ggparallel.Rd':
  'package-ggparallel-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.4Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'operator':
  'x' 'y'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Error(s) in re-building vignettes:
--- re-building 'ggsector.Rmd' using rmarkdown

Quitting from lines 32-38 [setup] (ggsector.Rmd)
Error: processing vignette 'ggsector.Rmd' failed with diagnostics:
package or namespace load failed for 'Seurat':
 object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'ggsector.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'decoration':
  'nudge_npcx' 'nudge_npcy'

Documented arguments not in \usage in documentation object 'generic_plot':
  'pc.out'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'ggplot_gtable':
  'plot'

Documented arguments not in \usage in documentation object 'zzz-internal':
  'latex' 'ggplot'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   8.3Mb
Documented arguments not in \usage in documentation object 'add_scale':
  'domain'

Documented arguments not in \usage in documentation object 'bin_vector':
  'width' 'origin' 'closed' 'pad'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    Giac  17.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/GIFT.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Unknown package 'IC2' in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'mlr3proba'
Argument items with no description in Rd object 'GLD.lm.full.surv':
  'maxit'
Argument items with no description in Rd object 'GLD.lm.surv':
  'maxit'
Documented arguments not in \usage in documentation object 'getBeta':
  'thetaConrol'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  14.3Mb
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/glmmSeq.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/glmmTMB.Rcheck/00install.out' for details.
Documented arguments not in \usage in documentation object 'glmpathcr-internal':
  'fit'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'fun.svd_1':
  'X'

Documented arguments not in \usage in documentation object 'fun.svd_2':
  'X'

Documented arguments not in \usage in documentation object 'fun.svd_3':
  'X'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/gmvjoint.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  'goodpractice-package.Rd'
Documented arguments not in \usage in documentation object 'doHttrRequest':
  'session' 'params'

Documented arguments not in \usage in documentation object 'get_google_token':
  'shiny_return_token'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/gosset.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
Documented arguments not in \usage in documentation object 'maxLevelBP':
  'org'

Documented arguments not in \usage in documentation object 'maxLevelCC':
  'org'

Documented arguments not in \usage in documentation object 'maxLevelMF':
  'org'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Invalid package aliases in Rd file '00.GPArotateDF.Rd':
  '00.GPArotateDF-package'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Documented arguments not in \usage in documentation object 'estimate_noise_nn':
  'n_thread'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'gvcm.cat'
Specified C++11: please drop specification unless essential
Unknown package 'gvcm.cat' in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.5Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> cleanEx()
> nameEx("gost")
> ### * gost
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: gost
> ### Title: Gene list functional enrichment.
> ### Aliases: gost
> 
> ### ** Examples
> 
> gostres <- gost(c("X:1000:1000000", "rs17396340", "GO:0005005", "ENSG00000156103", "NLRP1"))
> 
> 
> 
> 
> cleanEx()
> nameEx("gostplot")
> ### * gostplot
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: gostplot
> ### Title: Manhattan plot of functional enrichment results.
> ### Aliases: gostplot
> 
> ### ** Examples
> 
>  gostres <- gost(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/gps.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Missing or unexported objects:
  'Matrix::crossprod' 'Matrix::tcrossprod'
Running examples in 'GPvecchia-Ex.R' failed
The error most likely occurred in:

> ### Name: calculate_posterior_VL
> ### Title: Vecchia Laplace extension of GPVecchia for non-Gaussian data
> ### Aliases: calculate_posterior_VL
> 
> ### ** Examples
> 
> z=rnorm(10); locs=matrix(1:10,ncol=1); vecchia.approx=vecchia_specify(locs,m=5)
> calculate_posterior_VL(z,vecchia.approx,"gaussian",covparms=c(1,2,.5))
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'GPvecchia_vignette.Rmd' using rmarkdown

Quitting from lines 85-86 [paramm-est] (GPvecchia_vignette.Rmd)
Error: processing vignette 'GPvecchia_vignette.Rmd' failed with diagnostics:
'crossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'GPvecchia_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   5.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'fmpareto_HR_MLE':
  'method'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.4Mb
    libs   1.2Mb
Argument items with no description in Rd object 'HistPCA':
  'ggplot'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object 'load_map':
  'unity'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'prCaSetRownames':
  'rownames.fn'

Documented arguments not in \usage in documentation object 'prClearPCAclass':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
Error(s) in re-building vignettes:
--- re-building 'example_models.Rmd' using rmarkdown

Quitting from lines 45-46 [beetles_stan] (./../inst/examples/beetles.Rmd)

Quitting from lines NA-47 [unnamed-chunk-19] (./../inst/examples/beetles.Rmd)
Error: processing vignette 'example_models.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/stan-dev/example-models/master/bugs_examples/vol2/beetles/beetles_logit.stan'
--- failed re-building 'example_models.Rmd'

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

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

Quitting from lines 388-394 [plot_hidden] (get_started.Rmd)
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
`()` REASONS:
* Cannot currently use this function to produce a PNG file
* please install the `DiagrammeRsvg` package and retry
* pkg installed using `devtools::install_github('rich-iannone/DiagrammeRsvg')``()` REASONS:
* Cannot currently use this function to produce a PNG file
* please install the `DiagrammeRsvg` package and retry
* pkg installed using `devtools::install_github('rich-iannone/DiagrammeRsvg')`
--- failed re-building 'get_started.Rmd'

SUMMARY: processing the following files failed:
  'example_models.Rmd' 'get_started.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'doMC'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   2.7Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'groc.fit':
  'groc.fit'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'fit_grp.Rd':
  'grplasso-package'
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Objects in \usage without \alias in documentation object 'GSA-internal':
  'est.s0'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Invalid package aliases in Rd file 'gsb-package.Rd':
  'gsb-package'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/gsdensity.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) gsym.point.Rd:143: Escaped LaTeX specials: \&
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/gsynth.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) GUTS-package.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:201: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:209: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'traits':
  'efo_id' 'trait' 'uri'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'gwasrapidd-Ex.R' failed
The error most likely occurred in:

> ### Name: exists_variant
> ### Title: Check if a variant exists in the Catalog.
> ### Aliases: exists_variant
> 
> ### ** Examples
> 
> exists_variant('rs12345')
Error in `purrr::map()`:
ℹ In index: 1.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached: [www.ebi.ac.uk] Resolving timed out after 10002 milliseconds
Backtrace:
     ▆
  1. ├─gwasrapidd::exists_variant("rs12345")
  2. │ └─purrr::map(...)
  3. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  4. │     ├─purrr:::with_indexed_errors(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     ├─purrr:::call_with_cleanup(...)
  7. │     └─gwasrapidd (local) .f(.x[[i]], ...)
  8. │       └─gwasrapidd:::gc_request_all(...)
  9. │         └─gwasrapidd:::gc_request(...)
 10. │           └─httr::GET(url, user_agent_id)
 11. │             └─httr:::request_perform(req, hu$handle$handle)
 12. │               ├─httr:::request_fetch(req$output, req$url, handle)
 13. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 14. │                 └─curl::curl_fetch_memory(url, handle = handle)
 15. └─base::.handleSimpleError(...)
 16.   └─purrr (local) h(simpleError(msg, call))
 17.     └─cli::cli_abort(...)
 18.       └─rlang::abort(...)
Execution halted
checkRd: (-1) luzdat.Rd:21: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/gyro.Rcheck/00install.out' for details.
installed size is 250.2Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    java  247.1Mb
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### ** Examples
> 
> # Retrieve information about the jl user
> get_user_by_username("jl")
List of 5
 $ about    : chr "This is a test"
 $ created  : POSIXct[1:1], format: "2007-03-15 02:50:46"
 $ id       : chr "jl"
 $ karma    : int 4307
 $ submitted: int [1:850] 35686379 35675818 25172559 25172553 19464269 18498213 16659709 16659632 16659556 14237416 ...
 - attr(*, "class")= chr "hn_user"
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.34 0.11 5.08 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs    1.0Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
    doc     4.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/hal9001.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/haldensify.Rcheck/00install.out' for details.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.ga.breed' '.ga.fitness' '.ga.init' '.ga.mutate' '.ga.step'
  '.ga.weight'
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'haplo.em.fitter':
  'random.start '
Argument items with no description in Rd object 'haplo.model.frame':
  'control'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/haplotypes.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'modeling-package.Rd':
  'modeling-package'
checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   9.0Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) schools.Rd:18: Escaped LaTeX specials: \&
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
Documented arguments not in \usage in documentation object 'check_arg_for_hyperslab_func':
  'cur_arg'

Documented arguments not in \usage in documentation object 'extract_dim':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'compute_counts':
  'init' 'inflow'

Documented arguments not in \usage in documentation object 'compute_values':
  'counts'

Documented arguments not in \usage in documentation object 'create_demographic_table':
  '...'

Documented arguments not in \usage in documentation object 'eval_strategy_newdata':
  'model'

Documented arguments not in \usage in documentation object 'get_state_value_names':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    help      1.6Mb
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object 'autocomplete-defunct':
  'autocomplete'

Objects in \usage without \alias in documentation object 'set_auth-defunct':
  'set_auth'

Objects in \usage without \alias in documentation object 'set_proxy-defunct':
  'set_proxy'

Objects in \usage without \alias in documentation object 'traffic-defunct':
  'traffic'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/HeritSeq.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
Missing or unexported objects:
  'Matrix::crossprod' 'Matrix::tcrossprod'
Running examples in 'hero-Ex.R' failed
The error most likely occurred in:

> ### Name: assemble
> ### Title: Assemble spline ingredients for sandwich smooth
> ### Aliases: assemble assemble.hero_bspline assemble.hero_radspline
> ###   assemble.list
> 
> ### ** Examples
> 
> # construct b-spline
> object1 = bspline(nbasis = 10)
> # sequence to evaluate
> x1 = seq(0, 1, len = 11)
> # assemble b-spline information
> spline1 = assemble(object1, x1)
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
Documented arguments not in \usage in documentation object 'check.id_attributes':
  'inner_class'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'check_known_repos':
  'known_packages'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'defunct':
  'anova.mean' 'print.glht.mmc.multicomp' 'coef.arima.HH' 'glht.mmc'
  'plot.odds.ratio' 'persp.plane' 'persp.floor' 'persp.back.wall.x'
  'persp.back.wall.y' 'persp.setup' 'plot.hov' 'plot.hov.bf'
  'plot.matchMMC' 'seqplot.forecast'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Argument items with no description in Rd object 'residual.plots.lattice':
  'X'
Found export directives that require package 'methods':
  'exportClasses' 'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Argument items with no description in Rd object 'qcplate':
  'dat'
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'colorfulVennPlot'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/hilldiv.Rcheck/00install.out' for details.
Running examples in 'hillR-Ex.R' failed
The error most likely occurred in:

> ### Name: hill_phylo
> ### Title: Phylogenetic diversity through Hill Numbers
> ### Aliases: hill_phylo
> 
> ### ** Examples
> 
> comm = dummy = FD::dummy$abun
> tree = ape::rtree(n = ncol(comm), tip.label = paste0('sp', 1:8))
> hill_phylo(comm, tree, q = 0)
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Missing or unexported object: 'Matrix::tcrossprod'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/hisse.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object 'HistDAWass-package':
  \details: '...o use the package, including the most important functions ~~'
Invalid package aliases in Rd file 'histogram-package.Rd':
  'histogramtools-package'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'trackr'
Package which this enhances but not available for checking: 'HadoopStreaming'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.3Mb
html_describe_con: multiple local function definitions for 'g' with
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Argument items with no description in Rd object 'bpower':
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Argument items with no description in Rd object 'describe':
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Argument items with no description in Rd object 'find.matches':
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Argument items with no description in Rd object 'labcurve':
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Argument items with no description in Rd object 'varclus':
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Documented arguments not in \usage in documentation object 'bootstrapfun':
  'DoF' 'n_sample'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Missing or unexported objects:
  'Matrix::crossprod' 'Matrix::tcrossprod'
Auto-generated content requiring editing in Rd object 'HMVD-package':
  \details: '...o use the package, including the most important functions ~~'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
Invalid package aliases in Rd file 'hoardeR-package.Rd':
  'R/hoardeR-package'
Argument items with no description in Rd object 'bid2':
  'numattable1' 'playerseats1' 'blinds1' 'dealer1' 'b3' 'b4' 'round1'
  'ntable1' 'decision1'
Argument items with no description in Rd object 'calcwin1':
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Argument items with no description in Rd object 'mycount1':
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Argument items with no description in Rd object 'mygraphics1':
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  'b5' 'b6' 'b7' 'chips2' 'ntable1' 'myfast1' 'chipstart1' 'name1'
  'lowercut1'
Argument items with no description in Rd object 'nothing1':
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Argument items with no description in Rd object 'onepair1':
  'x'
Argument items with no description in Rd object 'straight1':
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Argument items with no description in Rd object 'straightdraw1':
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Argument items with no description in Rd object 'strflsh1':
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Argument items with no description in Rd object 'trip1':
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Argument items with no description in Rd object 'twopair1':
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Argument items with no description in Rd object 'writebets1':
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  'myfast1' 'name1'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    doc   3.3Mb
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'plot.hopitCP':
  'plotf'

Documented arguments not in \usage in documentation object 'sigma.hopit':
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Documented arguments not in \usage in documentation object 'summary.hopit':
  'control'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  'hpoPlot-package.Rd'
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object '.E3':
  'i' 'M'

Documented arguments not in \usage in documentation object '.E4':
  'i' 'M'

Documented arguments not in \usage in documentation object 'hrm.0w.2s':
  'group'

Documented arguments not in \usage in documentation object 'hrm.0w.3s':
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Documented arguments not in \usage in documentation object 'hrm.0w.4s':
  'group'

Documented arguments not in \usage in documentation object 'hrm.0w.5s':
  'group'

Documented arguments not in \usage in documentation object 'hrm.1f':
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Documented arguments not in \usage in documentation object 'hrm.1w.0f':
  'factor1'

Documented arguments not in \usage in documentation object 'hrm.2w.2f':
  'factor'

Documented arguments not in \usage in documentation object 'hrm.mv.1w.1f':
  'H' 'text'

Documented arguments not in \usage in documentation object 'hrm.mv.internal':
  'alpha' 'H' 'text'

Documented arguments not in \usage in documentation object 'hrm.test.1.none':
  'factor1' 'factor2'

Documented arguments not in \usage in documentation object 'hrm.test.1.one':
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Documented arguments not in \usage in documentation object 'hrm.test.2.one':
  'factor2'

Documented arguments not in \usage in documentation object 'hrm.test.2.two':
  'group'

Documented arguments not in \usage in documentation object 'hrm.test.3.three':
  'group'

Documented arguments not in \usage in documentation object 'hrm.test.4.four':
  'group'

Documented arguments not in \usage in documentation object 'hrm.test.5.five':
  'group'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'imageplot':
  '\dots'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'prGetStyle':
  'styles'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Argument items with no description in Rd object 'FramedHTML':
  'DiagnosticsPath'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    2.1Mb
Invalid package aliases in Rd file 'httkpop.Rd':
  'httkpop-package'
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
Documented arguments not in \usage in documentation object 'as.redactor':
  'expr'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'as.redactor':
  'expr'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'HydroMe-package.Rd':
  'HydroMe2-package'
checkRd: (-1) Trancura9414001.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) Trancura9414001.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) hydroPSO.Rd:390: Escaped LaTeX specials: \&
checkRd: (-1) hydroPSO.Rd:408: Escaped LaTeX specials: \&
installed size is  7.4Mb
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    extdata   5.5Mb
    libs      1.1Mb
installed size is  5.2Mb
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    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:7: Escaped LaTeX specials: \&
installed size is  6.2Mb
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installed size is  6.4Mb
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    doc   6.3Mb
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
Documented arguments not in \usage in documentation object 'scan.txt.Witec':
  'nwl' 'remove.zerospc'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Argument items with no description in Rd object 'print.Hypervolume':
  '...'
Argument items with no description in Rd object 'summary.Hypervolume':
  '...'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'fitting_epicurves.Rmd' using rmarkdown

Quitting from lines 56-60 [unnamed-chunk-4] (fitting_epicurves.Rmd)
Error: processing vignette 'fitting_epicurves.Rmd' failed with diagnostics:
The `date_index` of `x` must be a <Date> or <grates> object to use the provided `plot` method. Please raise an issue at https://github.com/reconverse/incidence2/issues If you would like another object <type> supported
--- failed re-building 'fitting_epicurves.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in documentation object 'btibgen':
  'ibdgen'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Argument items with no description in Rd object 'pairSum':
  'cov1' 'cov2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SparkR'
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ICAMS.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/iccCounts.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'icd'
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
S3 methods shown with full name in documentation object 'orlm':
  'orlm.forboot.fixed' 'orlm.forboot'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) pulmonary.Rd:13: Escaped LaTeX specials: \_
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Keywords: methods print
> 
> ### ** Examples
> 
> n <- 1000
> X <- cbind(rexp(n), rt(n,5), rnorm(n), rnorm(n), rnorm(n), rnorm(n))
> 
> test <- FOBIladle(X)
> summary(test)

FOBI Ladle estimator for X 
k:  2
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  36.48 2.03 38.53 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in documentation object 'internals':
  'iplotMain' 'segments.circle' 'griddat'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'internals':
  'plot.page'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'IFCdata'
Documented arguments not in \usage in documentation object 'fastAny':
  'obj'

Documented arguments not in \usage in documentation object 'getSTATSREPORT':
  '...'

Documented arguments not in \usage in documentation object 'split_feat':
  'operators'

Documented arguments not in \usage in documentation object 'toXML2_features_def':
  'features'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::tcrossprod'
Running examples in 'iGraphMatch-Ex.R' failed
The error most likely occurred in:

> ### Name: graph_match_Umeyama
> ### Title: Spectral Graph Matching Methods: Umeyama Algorithm
> ### Aliases: graph_match_Umeyama
> ### Keywords: internal
> 
> ### ** Examples
> 
> # match G_1 & G_2 using Umeyama algorithm
> G <- sample_correlated_gnp_pair(10, .9, .5)
> g1 <- G$graph1
> g2 <- G$graph2
> startm <- matrix(0, 10, 10)
> diag(startm)[1:4] <- 1
> 
> GM_Umeyama <- gm(g1, g2, similarity = startm, method = "Umeyama")
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   1.5Mb
    libs   6.2Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         1.4Mb
Documented arguments not in \usage in documentation object '.compl':
  'imgfile'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.2Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     10.1Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'image-package.Rd':
  'image-package'
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/imcExperiment.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/immunarch.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'accdata'
Documented arguments not in \usage in documentation object 'new_impactr_peaks':
  'acc_signal:'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  'imputeYn-package.Rd'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Missing or unexported object: 'Matrix::crossprod'
Running examples in 'influenceR-Ex.R' failed
The error most likely occurred in:

> ### Name: ens
> ### Title: Burt's Effective Network Size and Constraint index. The next two
> ###   functions below provide ways to measure the actors' access to
> ###   structural holes in a network. Structural holes "provide
> ###   opportunities to broker connections between people" (Burt 2008).
> ### Aliases: ens
> 
> ### ** Examples
> 
> ig.ex <- igraph::erdos.renyi.game(100, p.or.m=0.3) # generate an undirected 'igraph' object
> ens(ig.ex) # Effective Network Size scores for each node in the graph
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(influenceR)
  > 
  > test_check("influenceR")
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_metrics.R:9:3'): metrics work as expected ──────────────────────
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(influenceR::ens(flo_graph), flo_ens) at test_metrics.R:9:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─influenceR::ens(flo_graph)
  ── Error ('test_reference.R:57:3'): ens matches reference function ─────────────
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(influenceR::ens(flo_graph), ens_test(flo_graph)) at test_reference.R:57:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─influenceR::ens(flo_graph)
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
Problems with news in 'NEWS.md':
No news entries found.
Package which this enhances but not available for checking: 'gurobi'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Infusion.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Missing or unexported object: 'Matrix::crossprod'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Argument items with no description in Rd object 'combine.NULL':
  'x' 'y'
Argument items with no description in Rd object 'combine':
  'x' 'y'
Argument items with no description in Rd object 'combine.character':
  'x' 'y'
Argument items with no description in Rd object 'combine.list':
  'x' 'y'
Argument items with no description in Rd object 'findGeneric':
  'fname' 'envir'
Argument items with no description in Rd object 'fixPackageFileNames':
  'list'
Argument items with no description in Rd object 'forfun':
  'FUN'
Argument items with no description in Rd object 'get_S3_primitive_generics':
  'include_group_generics'
Argument items with no description in Rd object 'get_internal_S3_generics':
  'primitive'
Argument items with no description in Rd object 'is_primitive_in_base':
  'fname'
Argument items with no description in Rd object 'prefixed.lines':
  'src' '\dots'
Argument items with no description in Rd object 'print.allfun':
  'x' '\dots'
Argument items with no description in Rd object 'whole.word':
  '\dots'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Package suggested but not available for checking: 'cmdstanr'
Malformed Title field: should not end in a period.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/insurancerating.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/interflex.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/interplot.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'IntervalSurgeon-package':
  \seealso: 'Optional links to other man pages'
  \examples: '## Optional simple examples of the most important functions ...'
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.6Mb
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'selectRuleRRF':
  'target'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'rawAvgCost-deprecated':
  'cost.transf' 'in.millions' 'confidence.interval' 'minimum.year'
  'maximum.year' 'final.year' 'incomplete.year.threshold'
  'incomplete.year.weights' 'gam.k' 'mars.nprune' '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::tcrossprod'
Package suggested but not available for checking: 'surveyspec'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'chars_collapse':
  'collapse'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/IPDFileCheck.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'iprior_package.Rd':
  'iprior_package-package'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ips.Rcheck/00install.out' for details.
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/irtQ.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'print.cat_output':
  'object'

Documented arguments not in \usage in documentation object '[[<-,Itempool,numeric,missing-method':
  '...'

Documented arguments not in \usage in documentation object '[[<-,Response_set,numeric,missing-method':
  '...'

Documented arguments not in \usage in documentation object '[[<-,Testlet,numeric,missing-method':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'print.Item':
  'print.Item'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object 'islasso-internal':
  'modelX' '.checkinput' '.startpoint' '.islasso'
  'checkinput.islasso.path' 'startpoint.islasso.path'
  'islasso.path.fit.glm' 'islasso.path.fitter2' 'interpolate' 'makeHyp'
  'printHyp' 'cislasso' 'ci.fitted.islasso'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object '.assignmentMaker':
  '.precip_raster' '.precip_SD_raster'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/IsoriX.Rcheck/00install.out' for details.
Specified C++14: please drop specification unless essential
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    libs   2.8Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ivDiag.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'locClass'
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Invalid package aliases in Rd file 'ivprobit-package.Rd':
  'ivProbit-package'
Auto-generated content requiring editing in Rd object 'ivregEX-package':
  \references: '~~ Literature or other references for background information ~~'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          10.3Mb
GNU make is a SystemRequirements.
Rd files without \alias:
  'jackknifeKME-package.Rd'
Running examples in 'jackstraw-Ex.R' failed
The error most likely occurred in:

> ### Name: jackstraw_rpca
> ### Title: Non-Parametric Jackstraw for Principal Component Analysis (PCA)
> ###   using Randomized Singular Value Decomposition
> ### Aliases: jackstraw_rpca
> 
> ### ** Examples
> 
> ## simulate data from a latent variable model: Y = BL + E
> B = c(rep(1,10),rep(-1,10), rep(0,180))
> L = rnorm(20)
> E = matrix(rnorm(200*20), nrow=200)
> dat = B %*% t(L) + E
> dat = t(scale(t(dat), center=TRUE, scale=TRUE))
> 
> ## apply the jackstraw
> out = jackstraw_rpca(dat, r=1)
A number of null variables (s) to be permuted is not specified: s=round(0.10*m)=20.
A number of resampling iterations (B) is not specified: B=round(m*10/s)=100.
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(jackstraw)
  > 
  > test_check("jackstraw")
  [ FAIL 1 | WARN 13 | SKIP 0 | PASS 691 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-jackstraw.R:405:5'): jackstraw_rpca works ──────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(...) at test-jackstraw.R:405:4
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. ├─jackstraw::jackstraw_rpca(Xc, r = d, s = s, B = B, verbose = FALSE)
   10. └─base::loadNamespace(x)
   11.   └─base::namespaceImportFrom(...)
   12.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 1 | WARN 13 | SKIP 0 | PASS 691 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
Problems with news in 'NEWS.md':
No news entries found.
Running examples in 'JGL-Ex.R' failed
The error most likely occurred in:

> ### Name: net.edges
> ### Title: List the edges in a network
> ### Aliases: net.edges
> 
> ### ** Examples
> 
> ## load an example dataset with K=two classes, p=200 features, and n=100 samples per class:
> data(example.data)
> str(example.data)
List of 2
 $ : num [1:100, 1:200] 0.395 -2.03 -1.704 -0.469 1.75 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr [1:200] "gene 1" "gene 2" "gene 3" "gene 4" ...
 $ : num [1:100, 1:200] -1.548 1.45 -0.812 -0.589 0.69 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr [1:200] "gene 1" "gene 2" "gene 3" "gene 4" ...
> ## run fgl:
> fgl.results = JGL(Y=example.data,penalty="fused",lambda1=.25,lambda2=.1)
> ## get edges list:
> net.edges(fgl.results$theta)
[[1]]
+ 17/3052429 edges from 770aba9 (vertex names):
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    i18n   4.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: 'remMap'
Documented arguments not in \usage in documentation object 'paste_coef':
  'parlemts'

Documented arguments not in \usage in documentation object 'paste_linpred':
  'parlemts' 'matname'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/jrSiCKLSNMF.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  'karaoke-package.Rd'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/karyotapR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
prepare_Rd: NEWS.Rd:58: Dropping empty section 'kelvin INITIAL VERSION 1.0-0 (2012-05-30)'
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'covQualNested':
  'covBet'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'bw.abram.temp':
  'bw.abram.temp'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Missing or unexported object: 'Matrix::tcrossprod'
Documented arguments not in \usage in documentation object 'calc_PGtheta_R':
  'model' 'iter'

Documented arguments not in \usage in documentation object 'make_wsz_cpp':
  'info' 'initialized'

Documented arguments not in \usage in documentation object 'read_dfm_cpp':
  'W_raw'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'b_wincred_get':
  'backend'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [122s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(kiwisR)
  > 
  > test_check("kiwisR")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 50 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • Example KiWIS server offline. (1): 'test_ki_timeseries_values.R:26:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_ki_station_list.R:66:3'): ki_station_list accepts custom return fields (vector or string) ──
  <notSubsettableError/error/condition>
  Error in `raw$message`: object of type 'closure' is not subsettable
  Backtrace:
      ▆
   1. └─kiwisR::ki_station_list(hub = example_hub, return_fields = cust_ret_str) at test_ki_station_list.R:66:2
   2.   └─kiwisR:::check_ki_response(raw)
   3.     └─base::stop("Query returned error: ", raw$message)
   4.       └─base::.makeMessage(..., domain = domain)
   5.         └─base::lapply(list(...), as.character)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 50 ]
  Error: Test failures
  Execution halted
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'unlist.constr':
  'unlist.constr'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'knotR-package.Rd':
  'knot-package'
Package suggested but not available for checking: 'VARSEDIG'
Unknown package 'VARSEDIG' in Rd xrefs
'LazyData' is specified without a 'data' directory
Running examples in 'kofdata-Ex.R' failed
The error most likely occurred in:

> ### Name: download_cached_file
> ### Title: get_dataset
> ### Aliases: download_cached_file
> 
> ### ** Examples
> 
> f <-  download_cached_file("kofdatapkg", "313984fcd9f343d3961891319b0ed321",
+ "empty.txt",file.path(tempdir(),"empty.txt"))
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached: [datenservice.kof.ethz.ch] Resolving timed out after 10011 milliseconds
Calls: download_cached_file ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'stat.functions':
  'kappa.cor'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Documented arguments not in \usage in documentation object 'extract_and_augment_context':
  '...additional'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   1.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'ergm.userterms'
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package 'ergm.userterms' in Rd xrefs
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'akmedoids', 'clusterCrit'
Unknown packages 'clusterCrit', 'akmedoids' in Rd xrefs
Objects in \usage without \alias in documentation object 'latrend-generics':
  'nClusters' 'clusterProportions' 'clusterTrajectories' 'compose'
  'converged' 'externalMetric' 'estimationTime' 'fit'
  'fittedTrajectories' 'getArgumentDefaults' 'getArgumentExclusions'
  'getLabel' 'getLcMethod' 'getName' 'getShortName' 'idVariable'
  'metric' 'plotFittedTrajectories' 'plotClusterTrajectories' 'postFit'
  'postprob' 'predictAssignments' 'predictForCluster' 'predictPostprob'
  'prepareData' 'preFit' 'qqPlot' 'responseVariable' 'strip'
  'timeVariable' 'trajectoryAssignments' 'validate'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/lavaan.shiny.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'moments2':
  '...'

Documented arguments not in \usage in documentation object 'skeleton':
  'endogeneous' '...'

Documented arguments not in \usage in documentation object 'vcov2-internal':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    lcars.0.3.1
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'H_inv':
  'trunc'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Running examples in 'lcsm-Ex.R' failed
The error most likely occurred in:

> ### Name: plot_lcsm
> ### Title: Plot simplified path diagram of univariate and bivariate latent
> ###   change score models
> ### Aliases: plot_lcsm
> 
> ### ** Examples
> 
> # Simplified plot of univariate lcsm
> lavaan_syntax_uni <- fit_uni_lcsm(
+   data = data_bi_lcsm,
+   var = c("x1", "x2", "x3", "x4", "x5"),
+   model = list(
+     alpha_constant = TRUE,
+     beta = TRUE,
+     phi = TRUE
+   ),
+   return_lavaan_syntax = TRUE,
+   return_lavaan_syntax_string = TRUE
+ )
> 
> lavaan_object_uni <- fit_uni_lcsm(
+   data = data_bi_lcsm,
+   var = c("x1", "x2", "x3", "x4", "x5"),
+   model = list(
+     alpha_constant = TRUE,
+     beta = TRUE,
+     phi = TRUE
+   )
+ )
> 
> plot_lcsm(
+   lavaan_object = lavaan_object_uni,
+   what = "cons", whatLabels = "invisible",
+   lavaan_syntax = lavaan_syntax_uni,
+   lcsm = "univariate"
+ )
Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'lcsm-parameters.Rmd' using rmarkdown
--- finished re-building 'lcsm-parameters.Rmd'

--- re-building 'v0-longitudinal-plots.Rmd' using rmarkdown
--- finished re-building 'v0-longitudinal-plots.Rmd'

--- re-building 'v1-lavaan-syntax.Rmd' using rmarkdown
--- finished re-building 'v1-lavaan-syntax.Rmd'

--- re-building 'v2-path-diagrams.Rmd' using rmarkdown

Quitting from lines 47-70 [unnamed-chunk-2] (v2-path-diagrams.Rmd)
Error: processing vignette 'v2-path-diagrams.Rmd' failed with diagnostics:
objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
--- failed re-building 'v2-path-diagrams.Rmd'

--- re-building 'v3-extract-tutorial.Rmd' using rmarkdown
--- finished re-building 'v3-extract-tutorial.Rmd'

--- re-building 'v4-simulate-data.Rmd' using rmarkdown
--- finished re-building 'v4-simulate-data.Rmd'

SUMMARY: processing the following file failed:
  'v2-path-diagrams.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Missing or unexported objects:
  'Matrix::crossprod' 'Matrix::tcrossprod'
Documented arguments not in \usage in documentation object '.choose_best_subjects':
  'best' 'candidate'

Documented arguments not in \usage in documentation object '.normalize_props':
  'keep_all_items'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Argument items with no description in Rd object 'top.topic.words':
  'alpha'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/LDM.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Invalid package aliases in Rd file 'LEANR-package.Rd':
  'LEAN-package'
checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'learnn.Rd':
  'learnn-package'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/learnPopGen.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/lefko3.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'doMC'
Documented arguments not in \usage in documentation object 'backward_step':
  'empty_start_dataset' 'fit' '...'

Documented arguments not in \usage in documentation object 'backward_step_IM':
  'empty_start_dataset' 'fit' '...'

Documented arguments not in \usage in documentation object 'forward_step':
  'empty_start_dataset' 'fit' '...'

Documented arguments not in \usage in documentation object 'forward_step_IM':
  'empty_start_dataset' 'fit' '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Documented arguments not in \usage in documentation object 'lemon-ggproto':
  'side' 'is.primary'

Documented arguments not in \usage in documentation object 'render_gpar':
  'name'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'get_generic':
  'mismatch'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Error(s) in re-building vignettes:
--- re-building 'lfc_vignette.Rmd' using rmarkdown

Quitting from lines 35-47 [unnamed-chunk-1] (lfc_vignette.Rmd)
Error: processing vignette 'lfc_vignette.Rmd' failed with diagnostics:
package 'SummarizedExperiment' could not be loaded
--- failed re-building 'lfc_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/lfe.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'doMC'
Specified C++11: please drop specification unless essential
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installed size is  5.3Mb
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    libs   4.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'rsyslog'
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/liayson.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
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installed size is  5.6Mb
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    libs      1.7Mb
Documented arguments not in \usage in documentation object 'CoordInBounds':
  'direction'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.0Mb
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
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S3 methods shown with full name in documentation object 'BIC.threshold':
  'BIC.threshold'

S3 methods shown with full name in documentation object 'BIC.threshold.ggm':
  'BIC.threshold.ggm'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
Documented arguments not in \usage in documentation object 'MassAcylCer':
  'glccer'

Documented arguments not in \usage in documentation object 'MassPEo':
  'PEp'

Documented arguments not in \usage in documentation object 'findMS2precursor':
  'minint' 'maxint'

Documented arguments not in \usage in documentation object 'joinAnnotationResults':
  'simplifyAnnotation'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'get_variable':
  'x' 'name' 'mustExist' 'create'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/list.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs       1.4Mb
    testdata   1.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
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checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Specified C++11: please drop specification unless essential
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checkRd: (-1) SPSloess.Rd:71: Escaped LaTeX specials: \^ \^
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Invalid package aliases in Rd file 'Lock5Data-package.Rd':
  'Lock5Data-package'
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'spec.emb':
  'A'
Package suggested but not available for checking: 'rsyslog'
Package suggested but not available for checking: 'rsyslog'
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'dlogitnorm':
  'sigma'
Argument items with no description in Rd object 'invlogit':
  'q' '\dots'
Argument items with no description in Rd object 'logit':
  'p' '\dots'
Argument items with no description in Rd object 'plogitnorm':
  'sigma' '\dots'
Argument items with no description in Rd object 'qlogitnorm':
  'sigma' '\dots'
Argument items with no description in Rd object 'twCoefLogitnorm':
  '\dots'
Argument items with no description in Rd object 'twCoefLogitnormE':
  '\dots'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Argument items with no description in Rd object 'levopt':
  'x' 'alpha' 'fmax' 'tm'
Argument items with no description in Rd object 'pershow':
  'object'
Argument items with no description in Rd object 'norpt':
  'alist'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/LongDat.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/longsurr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'LoopAnalyst-package':
  \details: '...the package, including the most important ~~ ~~ functions ~~'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'importance_sampling.array':
  'is_method'

Documented arguments not in \usage in documentation object 'importance_sampling.default':
  'is_method'

Documented arguments not in \usage in documentation object 'importance_sampling.matrix':
  'is_method'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'scio'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'LotkasXX':
  'Table'
Argument items with no description in Rd object 'LotkasXY':
  'Table'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.0Mb
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'followx':
  'Xi' 'x0' 'h' 't0' 'iter' 'way' 'weights' 'pen' 'phi'
  'lasteigenvector' 'rho0' 'boundary' 'convergence.at' 'cross'
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Running examples in 'LRQMM-Ex.R' failed
The error most likely occurred in:

> ### Name: lrqmm
> ### Title: Fitting Linear Quantile Regression Mixed Models With
> ###   Relationship Matrix
> ### Aliases: lrqmm
> ### Keywords: quantile regression mixed models Frisch-Newton interior-point
> 
> ### ** Examples
> 
> #Start(not run)
> 
> 
> data(Cow)
> with(lrqmm(id=REGNO,sire=FREG,dam=MREG,X=HYS,Y=HL,cova=AGECAL,alpha=1,tau=0.5)
+ ,data=Cow)
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Package suggested but not available for checking: 'kerdiest'
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/LSX.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'setlogdata':
  'logdata'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/lvnet.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'depth'
'LazyData' is specified without a 'data' directory
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    gdal   2.9Mb
    libs  18.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/MAAPER.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'MACP_tutorial.Rmd' using rmarkdown

Quitting from lines 596-604 [unnamed-chunk-24] (MACP_tutorial.Rmd)
Error: processing vignette 'MACP_tutorial.Rmd' failed with diagnostics:
non-character argument
--- failed re-building 'MACP_tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'quitte'
Package suggested but not available for checking: 'doMC'
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    doc    6.2Mb
    libs  35.9Mb
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Argument items with no description in Rd object 'plot.magree':
  'xlab' 'ylab' 'main' '\dots'
Argument items with no description in Rd object 'print.summary.magree':
  'x' '\dots'
Argument items with no description in Rd object 'summary.magree':
  'object' '\dots'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### * listSpecies
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: listSpecies
> ### Title: list all species which have occurrence data within the MAP
> ###   database.
> ### Aliases: listSpecies
> 
> ### ** Examples
> 
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  2.13 0.2 2.33 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Argument items with no description in Rd object 'alignPeaks':
  '\dots'
'LazyData' is specified without a 'data' directory
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checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
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    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
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GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
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installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'map.scale':
  'x'
GNU make is a SystemRequirements.
checkRd: (-1) sw_sfac.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) Interpolation-class.Rd:41: Escaped LaTeX specials: \#
checkRd: (-1) MareyMap-class.Rd:85: Escaped LaTeX specials: \_
checkRd: (-1) MareyMap-methods.Rd:11: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) MareyMap-methods.Rd:12: Escaped LaTeX specials: \_
checkRd: (-1) SpeciesMaps-methods.Rd:11: Escaped LaTeX specials: \_
checkRd: (-1) interpolation-methods.Rd:13: Escaped LaTeX specials: \_
Argument items with no description in Rd object 'bias.factor':
  'RRud' 'RReu' 'rr' 's2'
'LazyData' is specified without a 'data' directory
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Undocumented S4 methods:
  generic 'crossprod' and siglist 'dgeMatrix,dtTMatrix'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'set.scale':
  'scale.dm' 'scale.par'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs       1.3Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'mark_my_dir':
  'mark_file'

Documented arguments not in \usage in documentation object 'path_type':
  'github_token'

Documented arguments not in \usage in documentation object 'read_assignment_yml':
  'path'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'marssTMB'
Objects in \usage without \alias in documentation object 'utility.functions':
  'fully.spec.x' 'marssMODEL.to.list'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'flashier'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'NewPackage-package.Rd':
  'NewPackage-package'
Auto-generated content requiring editing in Rd object 'NewPackage-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
Package suggested but not available for checking: 'gurobi'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.7Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'x_OP_y':
  'idxs'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'mr.smd':
  'structural.cost'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'mccca-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
'LazyData' is specified without a 'data' directory
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    libs   1.5Mb
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checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
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installed size is  5.1Mb
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Missing link or links in documentation object 'CoupledHeatedmcmcabn.Rd':
  '[abn:build_score_cache]{buildScoreCache}'
  '[abn:search_heuristic]{searchHeuristic}'

Missing link or links in documentation object 'abnCache_asia.Rd':
  '[abn:build_score_cache]{buildScoreCache}'

Missing link or links in documentation object 'mcmc.Rd':
  '[abn:build_score_cache]{buildScoreCache}'
  '[abn:search_heuristic]{searchHeuristic}'

Missing link or links in documentation object 'mcmc_asia.Rd':
  '[abn:build_score_cache]{buildScoreCache}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
Error(s) in re-building vignettes:
--- re-building 'mcmcabn.Rmd' using rmarkdown

Quitting from lines 143-149 [unnamed-chunk-7] (mcmcabn.Rmd)
Error: processing vignette 'mcmcabn.Rmd' failed with diagnostics:
`data.df` and `object` provided but can only accept one of them.
--- failed re-building 'mcmcabn.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  datablock.h:124:42: warning: pointer used after 'void operator delete(void*)' [-Wuse-after-free]
See 'd:/Rcompile/CRANpkg/local/4.4/MCMCpack.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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installed size is  7.4Mb
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    doc   6.8Mb
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'geom_cp_density':
  'include'

Documented arguments not in \usage in documentation object 'get_simulate':
  'par_trials' 'pars_pop' 'pars_varying'

Documented arguments not in \usage in documentation object 'pp_eval':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
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checkRd: (-1) omcdiag.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial version.
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'MethylCapSig'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    R     1.4Mb
    doc   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    libs      1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/merTools.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
GNU make is a SystemRequirements.
Invalid package aliases in Rd file 'taxa-package.Rd':
  'taxa-package'
Documented arguments not in \usage in documentation object 'limited_print':
  'trunc'

Documented arguments not in \usage in documentation object 'parse_heirarchies_to_taxonomy':
  'A'

Documented arguments not in \usage in documentation object 'parse_raw_heirarchies_to_taxonomy':
  'A'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'ClusterMF-deprecated':
  'formula' 'data' 'vi' 'study' 'whichweights' 'num.trees' 'mtry'
  'method' 'tau2'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'plot.metaplot_gtable':
  'y'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) dslp.Rd:11: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.2Mb
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Documented arguments not in \usage in documentation object 'wmata_api':
  'type' 'endpoint'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.6Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object '.gev.postpred':
  'vector'

Documented arguments not in \usage in documentation object '.gpd_2D_fit':
  '...other'

Documented arguments not in \usage in documentation object '.mvasym.check':
  'vector'

Documented arguments not in \usage in documentation object '.rPexstud':
  'Sigma'

Documented arguments not in \usage in documentation object '.rPsite':
  'index' 'param'

Documented arguments not in \usage in documentation object '.rdirspec':
  'rho'

Documented arguments not in \usage in documentation object '.rexstudspec':
  'index' 'Sigma'

Documented arguments not in \usage in documentation object '.rhrspec':
  'index'

Documented arguments not in \usage in documentation object '.rmevA1':
  'param'

Documented arguments not in \usage in documentation object '.rmevA2':
  'param'

Documented arguments not in \usage in documentation object '.rmevasy':
  'param'

Documented arguments not in \usage in documentation object '.rmevspec_cpp':
  'param'

Documented arguments not in \usage in documentation object '.wecdf':
  'ord'

Documented arguments not in \usage in documentation object 'tem.corr':
  'fran'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Missing or unexported objects:
  'Matrix::crossprod' 'Matrix::tcrossprod'
Running examples in 'MFPCA-Ex.R' failed
The error most likely occurred in:

> ### Name: MFPCA
> ### Title: Multivariate functional principal component analysis for
> ###   functions on different (dimensional) domains
> ### Aliases: MFPCA
> 
> ### ** Examples
> 
> oldPar <- par(no.readonly = TRUE)
> 
> set.seed(1)
> 
> ### simulate data (one-dimensional domains)
> sim <-  simMultiFunData(type = "split", argvals = list(seq(0,1,0.01), seq(-0.5,0.5,0.02)),
+                         M = 5, eFunType = "Poly", eValType = "linear", N = 100)
> 
> # MFPCA based on univariate FPCA
> uFPCA <- MFPCA(sim$simData, M = 5, uniExpansions = list(list(type = "uFPCA"),
+                                                                   list(type = "uFPCA")))
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Argument items with no description in Rd object 'predict.mfp':
  'safe'
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'Rpackage-package.Rd':
  'Rpackage-package'
Auto-generated content requiring editing in Rd object 'Rpackage-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'structSSI'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
S3 methods shown with full name in documentation object 'complete.miceadds':
  'complete.mids.nmi' 'complete.mids.1chain'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/micemd.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/microbial.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'microcontax.data'
Package unavailable to check Rd xrefs: 'microcontax.data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'changeDevSettings':
  'defaultsSettings'

Documented arguments not in \usage in documentation object 'getResultPerScheme':
  'criteria'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    lib    1.2Mb
    libs   1.2Mb
Argument items with no description in Rd object 'micSimParallel':
  'transitionMatrix' 'absStates' 'varInitStates' 'initStatesProb'
  'fixInitStates' 'maxAge' 'simHorizon' 'fertTr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'MIDASwrappeR-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '## Optional simple examples of the most important functions ...'
Package suggested but not available for checking: 'midfielddata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'migraph-Ex.R' failed
The error most likely occurred in:

> ### Name: core-periphery
> ### Title: Core-periphery clustering algorithms
> ### Aliases: core-periphery node_core
> 
> ### ** Examples
> 
> mpn_elite_usa_advice %>% as_tidygraph %>% 
+   mutate(corep = node_core(mpn_elite_usa_advice)) %>% 
+   autographr(node_color = "corep")
The Rgraphviz package is required to run this function. Would you like to install Rgraphviz from BioConductor? (Yes/no/cancel) 
The BiocManager package is required to run this function. Would you like to install BiocManager from CRAN? (Yes/no/cancel) 
Installing package into 'D:/temp/RtmpW0GAv7/RLIBS_21668205a127e'
(as 'lib' is unspecified)
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Calls: %>% ... thisRequiresBio -> thisRequires -> <Anonymous> -> contrib.url
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/migui.Rcheck/00install.out' for details.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: 'gurobi'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'getvol':
  'data'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
':::' call which should be '::': 'parallel:::detectCores'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/mi.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
GNU make is a SystemRequirements.
Missing or unexported object: 'Matrix::crossprod'
Running examples in 'MiRKAT-Ex.R' failed
The error most likely occurred in:

> ### Name: GLMMMiRKAT
> ### Title: The Microbiome Regression-based Kernel Association Test Based on
> ###   the Generalized Linear Mixed Model
> ### Aliases: GLMMMiRKAT
> 
> ### ** Examples
> 
> 
> 
> ## Example with Gaussian (e.g., body mass index) traits
> ## For non-Gaussian traits, see vignette. 
> 
> # Import example microbiome data with Gaussian traits
> data(nordata)
> otu.tab <- nordata$nor.otu.tab
> meta <- nordata$nor.meta
> 
> # Create kernel matrices and run analysis 
> if (requireNamespace("vegan")) {
+  library(vegan)
+  D_BC = as.matrix(vegdist(otu.tab, 'bray'))
+  K_BC = D2K(D_BC)
+  GLMMMiRKAT(y = meta$y, X = cbind(meta$x1, meta$x2), id = meta$id, 
+           Ks = K_BC, model = "gaussian", nperm = 500)
+ } else {
+ # Computation time is longer for phylogenetic kernels 
+  tree <- nordata$nor.tree
+  unifracs <- GUniFrac::GUniFrac(otu.tab, tree, alpha=c(1))$unifracs
+  D_W <- unifracs[,,"d_1"] 
+  K_W = D2K(D_W)
+  GLMMMiRKAT(y = meta$y, X = cbind(meta$x1, meta$x2), id = meta$id, 
+           Ks = K_W, model = "gaussian", nperm = 500)
+ }
Loading required package: permute
Loading required package: lattice
This is vegan 2.6-4
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'MiRKAT_Vignette.Rmd' using rmarkdown

Quitting from lines 347-354 [unnamed-chunk-21] (MiRKAT_Vignette.Rmd)
Error: processing vignette 'MiRKAT_Vignette.Rmd' failed with diagnostics:
'crossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'MiRKAT_Vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BRugs'
Documented arguments not in \usage in documentation object 'logAdd':
  'x' 'y'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/missCompare.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'l1_similarity'
Argument items with no description in Rd object 'randomizationTest':
  'R'
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Documented arguments not in \usage in documentation object 'mixAR-internal':
  'p' 'value' 'tau' 'etk' 'parscore' 'sigma' 'logpdf'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'rigaussian':
  'mu'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'Sn_A':
  'data'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/mixhvg.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
Auto-generated content requiring editing in Rd object 'mixl-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'mixRasch'
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    include   9.6Mb
    libs     17.0Mb
Running 'testthat.R' [88s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (requireNamespace("testthat", quietly = TRUE)) {
  +   library("testthat")
  +   library("mlr3learners")
  +   test_check("mlr3learners")
  + }
  Loading required package: mlr3
  # weights:  18 (10 variable)
  initial  value 164.791843 
  iter  10 value 16.177348
  iter  20 value 7.111438
  iter  30 value 6.182999
  iter  40 value 5.984028
  iter  50 value 5.961278
  iter  60 value 5.954900
  iter  70 value 5.951851
  iter  80 value 5.950343
  iter  90 value 5.949904
  iter 100 value 5.949867
  final  value 5.949867 
  stopped after 100 iterations
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 651 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_regr_ranger.R:7:3'): autotest ────────────────────────────────
  `result` is not TRUE
  
  `actual` is a list
  `expected` is a logical vector (TRUE)
  [predict()] learner 'regr.ranger:se' on task 'feat_single_logical' failed: predict log has errors: 'tcrossprod' is not an exported object from 'namespace:Matrix'
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 651 ]
  Error: Test failures
  Execution halted
Documented arguments not in \usage in documentation object 'mlr_assertions':
  'resample_result'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'cpoTemplate':
  'affect.names'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/mlt.docreg.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/mlt.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/mlVAR.Rcheck/00install.out' for details.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Problems with news in 'NEWS.md':
No news entries found.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/MM2S.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/mMARCH.AC.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'mmeln-package':
  \details: '...the package, including the most important ~~ ~~ functions ~~'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    5.9Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/mnet.Rcheck/00install.out' for details.
Rd files without \alias:
  'mnlfa-package.Rd'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Flury'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Packages suggested but not available for checking:
  'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene'
Documented arguments not in \usage in documentation object 'simplifiedSampleTile':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'check_augment_data_specification':
  'strict'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Running examples in 'modnets-Ex.R' failed
The error most likely occurred in:

> ### Name: intsPlot
> ### Title: Plot confidence intervals for interaction terms
> ### Aliases: intsPlot
> 
> ### ** Examples
> 
> fit <- fitNetwork(ggmDat, 'M')
> plot(fit, 'ints', y = 'all')
Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: no function found corresponding to methods exports from 'moko' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    * efourier with default norm=TRUE now messages about how wrong it may be
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
Argument items with no description in Rd object 'as.difftime':
  'tim' 'format'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/MonoPhy.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/morphomap.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Morpho.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'create_barrier_cs':
  'fields'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'corpus.useR.2008.abstracts'
Specified C++11: please drop specification unless essential
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
Rd files without \alias:
  'MPLikelihoodWB-package.Rd'
Documented arguments not in \usage in documentation object 'addHeaderToSavedata':
  'director'

Documented arguments not in \usage in documentation object 'extractIndirect':
  'curFile'

Documented arguments not in \usage in documentation object 'extractIndirect_section':
  'curFile'

Documented arguments not in \usage in documentation object 'graphModel':
  'The'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object 'internals':
  'check.in' 'check.out' 'start.theta' 'iMqr.internal' 'cov.theta'
  'iobjfun' 'sortH' 'isigma' 'iMqr.newton' 'num.fun' 'make.bfun'
  'apply_bfun' 'p.bisec' 'slp.basis' 'is.slp' 'iqr.waldtest'
  'extract.p' 'pred.beta' 'print.iMqr' 'print.summary.iMqr'
  'terms.iMqr' 'model.matrix.iMqr' 'vcov.iMqr' 'nobs.iMqr'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) F.huggins.estim.Rd:199: Escaped LaTeX specials: \$ \$
checkRd: (-1) F.huggins.estim.Rd:205: Escaped LaTeX specials: \$
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checkRd: (-1) lines.cjs.Rd:15: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
Auto-generated content requiring editing in Rd object 'mrbsizer-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/MSCquartets.Rcheck/00install.out' for details.
Argument items with no description in Rd object 'msda':
  'sml'
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    data   4.5Mb
    libs   1.2Mb
Documented arguments not in \usage in documentation object 'CalcMPDynamics':
  'M_ageArray' 'TAC_f' 'E_f' 'SizeLim_f' 'FinF' 'Spat_targ'
  'CAL_binsmid' 'Linf' 'Len_age' 'maxage' 'nareas' 'Asize' 'nCALbins'
  'qs' 'qvar' 'qinc'

Documented arguments not in \usage in documentation object 'popdynCPP':
  'SSBcurr'

Documented arguments not in \usage in documentation object 'popdynOneMICE':
  'nyears'

Documented arguments not in \usage in documentation object 'qestMICE':
  'mod' 'plusgroup.' 'WtC'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(mSigTools)
  > 
  > test_check("mSigTools")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 42 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_optimize_exposure_QP.R:4:3'): optimize_exposure_QP ─────────────
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. └─base::loadNamespace(x) at test_optimize_exposure_QP.R:4:2
    2.   ├─base::namespaceImportFrom(...)
    3.   │ └─base::asNamespace(ns)
    4.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    5.     ├─base::namespaceImport(...)
    6.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.       ├─base::namespaceImportClasses(...)
    8.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
    9.       │ │ └─base::asNamespace(ns)
   10.       │ └─base::asNamespace(ns)
   11.       └─base::loadNamespace(...)
   12.         ├─base::namespaceImport(...)
   13.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   14.           ├─base::namespaceImport(...)
   15.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   16.             └─base::namespaceImportFrom(...)
   17.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 42 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Argument items with no description in Rd object 'DAGOSTINO':
  'data'
Argument items with no description in Rd object 'HZ.test':
  'data'
Argument items with no description in Rd object 'MardiaTest':
  'data'
Argument items with no description in Rd object 'Royston.test':
  'data'
Argument items with no description in Rd object 'gen.var':
  '\dots'
Argument items with no description in Rd object 'larg.ellip':
  'n' 'box' 'add' 'xlim' 'ylim' 'zlim' 'xlab' 'ylab' 'zlab' 'col'
  'alpha' '\dots'
Argument items with no description in Rd object 'prism':
  'add'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
Invalid package aliases in Rd file 'ms_sev-package.Rd':
  'ms_sev-package'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/MTAR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'pca.plot.wrap':
  'lda.plot.wrap.1'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'mtscr-Ex.R' failed
The error most likely occurred in:

> ### Name: mtscr_model
> ### Title: Create MTS model
> ### Aliases: mtscr_model
> 
> ### ** Examples
> 
> data("mtscr_creativity", package = "mtscr")
> 
> mtscr_creativity <- mtscr_creativity |>
+   dplyr::slice_sample(n = 300) # for performance, ignore
> 
> mtscr_model(mtscr_creativity, id, item, SemDis_MEAN) |>
+   summary()
Error in `purrr::map()`:
ℹ In index: 1.
Caused by error:
! object 'crossprod' is not exported by 'namespace:Matrix'
Backtrace:
     ▆
  1. ├─base::summary(mtscr_model(mtscr_creativity, id, item, SemDis_MEAN))
  2. ├─mtscr::mtscr_model(mtscr_creativity, id, item, SemDis_MEAN)
  3. │ └─purrr::map(...)
  4. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  5. │     ├─purrr:::with_indexed_errors(...)
  6. │     │ └─base::withCallingHandlers(...)
  7. │     ├─purrr:::call_with_cleanup(...)
  8. │     └─mtscr (local) .f(.x[[i]], ...)
  9. ├─base::loadNamespace(x)
 10. │ └─base::namespaceImportFrom(...)
 11. │   └─base::importIntoEnv(impenv, impnames, ns, impvars)
 12. │     └─base::stop(...)
 13. └─base::.handleSimpleError(...)
 14.   └─purrr (local) h(simpleError(msg, call))
 15.     └─cli::cli_abort(...)
 16.       └─rlang::abort(...)
Execution halted
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'diagPlot':
  'hvt.results.model'

Documented arguments not in \usage in documentation object 'getOptimalCentroids':
  'depth'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) MultBiplotR-package.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) MultBiplotR-package.Rd:52: Escaped LaTeX specials: \&
Argument items with no description in Rd object 'BinaryLogBiplotJoint':
  'lambda'
Argument items with no description in Rd object 'ConstrainedOrdinalLogisticBiplot':
  'show'
Argument items with no description in Rd object 'ContinuousProximities':
  'ysup'
Argument items with no description in Rd object 'Multiquad':
  'nnodes' 'dims'
Argument items with no description in Rd object 'PLSR1Bin':
  'grouping'
Argument items with no description in Rd object 'Unfolding':
  'lambda' 'omega' 'plot'
Argument items with no description in Rd object 'plot.CCA.sol':
  'x' 'A1' 'A2' 'ShowAxis' 'margin' 'PlotSites' 'PlotSpecies' 'PlotEnv'
  'LabelSites' 'LabelSpecies' 'LabelEnv' 'TypeSites' 'SpeciesQuality'
  'MinQualityVars' 'dp' 'pr' 'PlotAxis' 'TypeScale' 'ValuesScale'
  'mode' 'CexSites' 'CexSpecies' 'CexVar' 'ColorSites' 'ColorSpecies'
  'ColorVar' 'PchSites' 'PchSpecies' 'PchVar' 'SizeQualSites'
  'SizeQualSpecies' 'SizeQualVars' 'ColorQualSites' 'ColorQualSpecies'
  'ColorQualVars' 'SmartLabels'
Argument items with no description in Rd object 'plot.CanonicalDistanceAnalysis':
  'SmartLabels'
Argument items with no description in Rd object 'plot.Principal.Coordinates':
  'ShowAxis' 'PlotBinaryMeans' 'MinIncidence' 'ShowBox'
  'ColorSupContVars' 'ColorSupBinVars' 'ColorSupOrdVars' 'TypeScale'
  'SupMode' 'PlotSupVars'
Argument items with no description in Rd object 'plot.Unfolding':
  'SpeciesQuality' 'dp' 'PlotAxis' 'TypeScale' 'ValuesScale' 'mode'
  'CexSites' 'CexSpecies' 'CexVar' 'ColorSites' 'ColorSpecies'
  'ColorVar' 'PchSites' 'PchSpecies' 'PchVar' 'SizeQualSites'
  'SizeQualSpecies' 'SizeQualVars' 'ColorQualSites' 'ColorQualSpecies'
  'ColorQualVars' 'SmartLabels' 'PlotTol' '...'
Argument items with no description in Rd object 'scores.CCA.sol':
  'CCA.sol'
Argument items with no description in Rd object 'summary.Canonical.Biplot':
  'object'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'plotBoxes':
  'lwd' 'T.base' 'font.family' 'fig' 'mar'

Documented arguments not in \usage in documentation object 'plotLetters':
  'width' 'lwd' 'label.groups' 'T.base' 'orientation'

Documented arguments not in \usage in documentation object 'plotTs':
  'font.family' 'fig' 'mar'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/multiblock.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/multibridge.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in 'multifamm-Ex.R' failed
The error most likely occurred in:

> ### Name: multiFAMM
> ### Title: Multivariate Functional Additive Mixed Model Regression
> ### Aliases: multiFAMM
> 
> ### ** Examples
> 
> 
> # subset of the phonetic data (very small subset, no meaningful results can
> # be expected and no random effects other than the random smooth should be
> # included in the model)
> 
> data(phonetic_subset)
> 
> m <- multiFAMM(data = phonetic_subset, covariate = TRUE, num_covariates = 2,
+                covariate_form = c("by", "by"), interaction = TRUE,
+                which_interaction = matrix(c(FALSE, TRUE, TRUE, FALSE),
+                nrow = 2, ncol = 2), bf_covs = c(5), m_covs = list(c(2, 3)),
+                mfpc_cut_method = "total_var", final_method = "w_bam")
--------------------------------------
sparseFLMM for Dimension aco 
--------------------------------------
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Documented arguments not in \usage in documentation object 'Trace':
  'x'

Documented arguments not in \usage in documentation object 'iteraite_fun_Iter':
  'The'

Documented arguments not in \usage in documentation object 'prepare_data':
  'The'

Documented arguments not in \usage in documentation object 'project':
  'x'

Documented arguments not in \usage in documentation object 'select_initial_Iter':
  'X' 'parametrs'

Documented arguments not in \usage in documentation object 'similarity_function':
  'x'

Documented arguments not in \usage in documentation object 'similarity_noncum':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'cmdstanr'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   6.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rrelaxiv'
Running examples in 'multipanelfigure-Ex.R' failed
The error most likely occurred in:

> ### Name: images
> ### Title: Images
> ### Aliases: images rhino unicorn
> 
> ### ** Examples
> 
> figure <- multi_panel_figure(
+   width = c(60, 40, 40), height = c(40, 40, 40)
+ )
> image_files <- system.file("extdata", package = "multipanelfigure") %>%
+   dir(full.names = TRUE) %>%
+   setNames(basename(.))
> figure %>%
+   fill_panel(image_files["farouq.tiff"]) %>%
+   fill_panel(image_files["unicorn.svg"], column = 2:3) %>%
+   fill_panel(image_files["rhino.jpg"], row = 2:3) %>%
+   fill_panel(image_files["Rlogo.png"], column = 2:3, row = 2:3)
Setting row to 1
Setting column to 1
Warning in warn_about_file.access_under_windows() :
  This function depends on file.access, which can give unexpected results under Windows.
Setting row to 1
Warning in warn_about_file.access_under_windows() :
  This function depends on file.access, which can give unexpected results under Windows.
Error: Rterm.exe: FailedToExecuteCommand `"inkscape" "D:/temp/Rtmp0SzCv7/magick-PxWIVESIEZq4OXtXoZKBbSja1AjFfD6R" --export-png="D:/temp/Rtmp0SzCv7/magick-FeeAER0vkTbAPsAOfClI-RLsSHRWU3qg.png" --export-dpi="300" --export-background="rgb(100%,100%,100%)" --export-background-opacity="1" > "D:/temp/Rtmp0SzCv7/magick-vzu5aP-xaIbEuBQv5tte1KdoRqp6bwD1" 2>&1' (-1) @ error/delegate.c/ExternalDelegateCommand/514
Execution halted
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'check_mnsl':
  'fix'

Documented arguments not in \usage in documentation object 'text_colour':
  'a'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/mvMORPH.Rcheck/00install.out' for details.
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rTubeDB'
Package unavailable to check Rd xrefs: 'rTubeDB'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'asreml'
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::tcrossprod'
Package suggested but not available for checking: 're2r'
Argument items with no description in Rd object 'check_subject_pattern':
  'subject.vec' 'pattern'
Argument items with no description in Rd object 'names_or_error':
  'pattern'
Argument items with no description in Rd object 'only_captures':
  'match.mat' 'pattern'
Argument items with no description in Rd object 'stop_for_names':
  'pattern'
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     2.4Mb
    models   1.1Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spatialClust'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.7Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    6.5Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
Invalid package aliases in Rd file 'NBBttest-package.Rd':
  'NBBtatest-package'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/NCC.Rcheck/00install.out' for details.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Documented arguments not in \usage in documentation object 'Moth':
  'delta.ident'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'assignClasses':
  'df'

Documented arguments not in \usage in documentation object 'dateConvert':
  'use_fasstime'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Error(s) in re-building vignettes:
--- re-building 'neotoma2-package.Rmd' using rmarkdown

Quitting from lines 77-84 [getSiteBySiteID] (neotoma2-package.Rmd)
Error: processing vignette 'neotoma2-package.Rmd' failed with diagnostics:
object 'response' not found
--- failed re-building 'neotoma2-package.Rmd'

SUMMARY: processing the following file failed:
  'neotoma2-package.Rmd'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Missing or unexported object: 'Matrix::crossprod'
Running examples in 'net4pg-Ex.R' failed
The error most likely occurred in:

> ### Name: cc_composition
> ### Title: Get peptides and peptide-to-protein mappings for each connected
> ###   component
> ### Aliases: cc_composition
> 
> ### ** Examples
> 
> # Read the tab-delimited file containing the proteome incidence matrix
> incM_filename <- system.file("extdata"
+                              , "incM_example"
+                              , package = "net4pg"
+                              , mustWork = TRUE)
> rownames_filename <- system.file("extdata"
+                                   , "peptideIDs_incM_example"
+                                   , package = "net4pg"
+                                   , mustWork = TRUE)
> colnames_filename <- system.file("extdata"
+                                  , "proteinIDs_incM_example"
+                                  , package = "net4pg"
+                                  , mustWork = TRUE)
> incM <- read_inc_matrix(incM_filename = incM_filename
+                  , colnames_filename = colnames_filename
+                  , rownames_filename = rownames_filename)
> # Only retain proteins with at least one shared peptide and all peptides
> # mapping on such proteins.
> incM_reduced <- reduce_inc_matrix(incM)
> # Generate adjacency matrix describing protein-to-protein mappings
> adjM <- get_adj_matrix(incM_reduced)
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Intro_To_net4pg.Rmd' using rmarkdown

Quitting from lines 198-200 [unnamed-chunk-5] (Intro_To_net4pg.Rmd)
Error: processing vignette 'Intro_To_net4pg.Rmd' failed with diagnostics:
'crossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'Intro_To_net4pg.Rmd'

SUMMARY: processing the following file failed:
  'Intro_To_net4pg.Rmd'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
':::' call which should be '::': 'lhs:::maximinLHS'
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_ \_
checkRd: (-1) makeNetwork.Rd:31: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'print.networkDynamic':
  '\dots'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'network-internal':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
GNU make is a SystemRequirements.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> try1 = zscore_img(img, margin=1)
> stopifnot(all.equal(try1, truth1))
>   
> z = zscore_img(img, margin=NULL)
> ztrim = zscore_img(img, margin=NULL, 
+ centrality = "trimmed_mean", variability = "trimmed_sd")
> 
> z = zscore_img(img, centrality = "median", variability = "iqr")
> z = zscore_img(img, centrality = "median", variability = "iqrdiff")
> z = zscore_img(img, centrality = "median", variability = "maddiff")
> 
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  11.35 0.75 12.16 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::tcrossprod'
Running examples in 'newsmap-Ex.R' failed
The error most likely occurred in:

> ### Name: textmodel_newsmap
> ### Title: Semi-supervised Bayesian multinomial model for geographical
> ###   document classification
> ### Aliases: textmodel_newsmap
> 
> ### ** Examples
> 
> require(quanteda)
Loading required package: quanteda
Package version: 3.3.1
Unicode version: 13.0
ICU version: 69.1
Parallel computing: 2 of 96 threads used.
See https://quanteda.io for tutorials and examples.
> text_en <- c(text1 = "This is an article about Ireland.",
+              text2 = "The South Korean prime minister was re-elected.")
> 
> toks_en <- tokens(text_en)
> label_toks_en <- tokens_lookup(toks_en, data_dictionary_newsmap_en, levels = 3)
> label_dfm_en <- dfm(label_toks_en)
> 
> feat_dfm_en <- dfm(toks_en, tolower = FALSE)
> 
> model_en <- textmodel_newsmap(feat_dfm_en, label_dfm_en)
> predict(model_en)
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Found the following significant warnings:
  Warning: GitHub.com seems offline, and `options(nfl4th.keep_games)` is not set to TRUE. Deleting the games cache, and predictions may not be available without an internet connection.
See 'd:/Rcompile/CRANpkg/local/4.4/nfl4th.Rcheck/00install.out' for details.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'NH-MSAR-package.Rd':
  'NH-MSAR-package'
Argument items with no description in Rd object 'ENu_graph':
  'N.s.data'
Argument items with no description in Rd object 'Estep.MSAR.VM':
  'verbose'
Auto-generated content requiring editing in Rd object 'NH-MSAR-package':
  \details: '...the package, including the most important ~~ ~~ functions ~~'
Argument items with no description in Rd object 'init.theta.MSAR (NH-MSAR)':
  '\dots'
Argument items with no description in Rd object 'init.theta.MSAR.VM':
  '\dots'
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/nichevol.Rcheck/00install.out' for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    CppCode   4.7Mb
    R         7.4Mb
    include  10.5Mb
    libs      1.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Package which this enhances but not available for checking: 'jpndistrict'
Malformed Description field: should contain one or more complete sentences.
Objects in \usage without \alias in documentation object 'getPossibleR':
  'brkCalc' 'findPowerR'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'njgeo-Ex.R' failed
The error most likely occurred in:

> ### Name: geocode_address_candidates
> ### Title: Geocode an address and retrieve all candidates using the NJOGIS
> ###   ArcGIS REST API
> ### Aliases: geocode_address_candidates
> 
> ### ** Examples
> 
> geocode_address_candidates(address = "33 Livingston Ave", city = "New Brunswick")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [geo.nj.gov] Resolving timed out after 10005 milliseconds
Calls: geocode_address_candidates ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/nlcv.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.7Mb
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
Documented arguments not in \usage in documentation object 'nldoc_write_nldoc':
  'number_ections'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) nltm.control.Rd:29: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Documented arguments not in \usage in documentation object 'ccSpec':
  'a'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object 'NMOF-internal':
  'mRU' 'mRN' 'mcList' 'repair1c'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'logistf-package.Rd':
  'logistf-package' '{logistf}-package'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'substitution_models.Rmd' using rmarkdown

Quitting from lines 47-61 [start] (substitution_models.Rmd)
Error: processing vignette 'substitution_models.Rmd' failed with diagnostics:
object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'substitution_models.Rmd'

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

Quitting from lines 26-40 [create alignment] (workflow.Rmd)
Error: processing vignette 'workflow.Rmd' failed with diagnostics:
object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'workflow.Rmd'

SUMMARY: processing the following files failed:
  'substitution_models.Rmd' 'workflow.Rmd'

Error: Vignette re-building failed.
Execution halted
Auto-generated content requiring editing in Rd object 'noise-package':
  \details: '...the package, including the most important ~~ ~~ functions ~~'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'get_max_stat':
  'statfunc'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'StatQQVPC':
  'mapping' 'data' 'geom' 'position' 'na.rm' 'show.legend'
  'inherit.aes' '...'

Documented arguments not in \usage in documentation object 'StatQQnorm':
  'mapping' 'data' 'geom' 'position' 'na.rm' 'show.legend'
  'inherit.aes' '...'

Documented arguments not in \usage in documentation object 'StatQQrefline':
  'mapping' 'data' 'geom' 'position' 'na.rm' 'show.legend'
  'inherit.aes' '...'

Documented arguments not in \usage in documentation object 'covload.sub.table':
  'nrows'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.6Mb
    mods   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> nameEx("cast_geo")
> ### * cast_geo
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: cast_geo
> ### Title: Cast geo granularity from API
> ### Aliases: cast_geo
> 
> ### ** Examples
> 
> ## Not run: 
> ##D  DT <- cast_geo(2020)
> ## End(Not run)
> 
> 
> 
> cleanEx()
> nameEx("get_change")
> ### * get_change
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: get_change
> ### Title: Get geo code changes with API
> ### Aliases: get_change
> 
> ### ** Examples
> 
> DT <- get_change("kommune", from = 2018, to = 2020)
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
Running examples in 'NormData-Ex.R' failed
The error most likely occurred in:

> ### Name: GLT
> ### Title: Conduct the General Linear Test (GLT) procedure
> ### Aliases: GLT
> ### Keywords: Fitted model GLT General Linear Test F test-statistic
> 
> ### ** Examples
> 
> # Replicate the GLT results that were obtained in 
> # Case study 1 of Chapter 5 in Van der Elst (2023)
> # ------------------------------------------------
> data(Personality)
> 
> GLT.Openness <- GLT(Dataset=Personality,
+      Unrestricted.Model=Openness~LE, Restricted.Model=Openness~1)
Error in crossprod(rval) : "crossprod" is not a BUILTIN function
Calls: GLT ... waldtest.lm -> <Anonymous> -> vcovHC.default -> meatHC
Execution halted
Auto-generated content requiring editing in Rd object 'nose-package':
  \details: '...the package, including the most important ~~ ~~ functions ~~'
Documented arguments not in \usage in documentation object 'FunctionSanityChecks':
  'structure'

Documented arguments not in \usage in documentation object 'newLine':
  'current.in'

Documented arguments not in \usage in documentation object 'nosoiSimConstructor':
  'pres.time'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Running examples in 'novelforestSG-Ex.R' failed
The error most likely occurred in:

> ### Name: backtransform
> ### Title: Backtransform Scaled Predictors
> ### Aliases: backtransform
> 
> ### ** Examples
> 
> # download the model object containing input data
> novelforest_model <- download_model()
To save the model locally, use argument save_to = 'path/filename.rds'
Downloading model (size: 16.5 Mb)
Warning in readRDS(file = url("https://github.com/hrlai/novelforestSG/blob/master/data/novelforest_model.rds?raw=true")) :
  URL 'https://raw.githubusercontent.com/hrlai/novelforestSG/master/data/novelforest_model.rds': Timeout of 60 seconds was reached
Error in readRDS(file = url("https://github.com/hrlai/novelforestSG/blob/master/data/novelforest_model.rds?raw=true")) : 
  cannot open the connection to 'https://github.com/hrlai/novelforestSG/blob/master/data/novelforest_model.rds?raw=true'
Calls: download_model -> readRDS
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'read':
  'dots'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Documented arguments not in \usage in documentation object 'Create_P':
  'y_zx_dependent'

Documented arguments not in \usage in documentation object 'make_proposer':
  'N'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ardechedata.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) nsRFA-package.Rd:231: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/numbat.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    doc       5.7Mb
    extdata   1.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
Documented arguments not in \usage in documentation object 'cust.colorbar':
  '\code{input.mode}' '\code{force.figdim.widget}' '\code{xpos}'
  'region'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.0Mb
    libs   1.3Mb
Argument items with no description in Rd object 'plot.comphat':
  '\dots'
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
Downloaded: 0.58 MB  
Downloaded: 0.58 MB  
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Downloaded: 0.58 MB  
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Downloaded: 0.58 MB  
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Downloaded: 0.58 MB  
Downloaded: 0.58 MB  
Downloaded: 0.58 MB  
======== End of example output (where/before crash/hang up occured ?) ========
Rd files without \alias:
  'odbc-package.Rd'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> gene_data <- KEGG_gather(gene_data)
 / /
 L_L_
/    \
|00  |       _______
|_/  |      /  ___  \
|    |     /  /   \  \
|    |_____\  \_  /  /
 \          \____/  /_____
  \ _______________/______\................please be patient =)
OK (HTTP 200). / /
 L_L_
/    \
|00  |       _______
|_/  |      /  ___  \
|    |     /  /   \  \
|    |_____\  \_  /  /
 \          \____/  /_____
  \ _______________/______\................please be patient =)
OK (HTTP 200).OK (HTTP 200).> 
> gene_data <- KEGG_gather(gene_data)
 / /
 L_L_
/    \
|00  |       _______
|_/  |      /  ___  \
|    |     /  /   \  \
|    |_____\  \_  /  /
 \          \____/  /_____
  \ _______________/______\................please be patient =)
======== End of example output (where/before crash/hang up occured ?) ========
Package suggested but not available for checking: 'cmdstanr'
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/oncoPredict.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Rd files without \alias:
  'ontologyPlot-package.Rd'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/OpenCL.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'unix'
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs   13.1Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'unary_ops':
  'log10.ProcessNode' 'log10.ProcessGraphParameter'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    R        2.6Mb
    data     1.4Mb
    libs     4.9Mb
    models   4.8Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Package suggested but not available for checking: 'openNLPmodels.en'
Documented arguments not in \usage in documentation object 'clique_color_pals':
  'aplha'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'bertinBase':
  'x' 'ratings' 'trim'

Documented arguments not in \usage in documentation object 'biplot3dBase2':
  'ext.sphere'

Documented arguments not in \usage in documentation object 'convertImportObjectToRepGridObject':
  'x'

Documented arguments not in \usage in documentation object 'convertScivescoImportObjectToRepGridObject':
  'x'

Documented arguments not in \usage in documentation object 'mapCoordinatesToColor':
  'color'

Documented arguments not in \usage in documentation object 'quasiDistributionDistanceSlater':
  'rep'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.7Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
Documented arguments not in \usage in documentation object 'assign_binIDs':
  'id:' 'binID:' 'lastbit:'

Documented arguments not in \usage in documentation object 'calcCatchmArea_assignNetID':
  'netID'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      1.4Mb
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'gurobi'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Package suggested but not available for checking: 'rrelaxiv'
Package suggested but not available for checking: 'gurobi'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'dsevdist':
  'x' 'sevdist'
Running examples in 'OralOpioids-Ex.R' failed
The error most likely occurred in:

> ### Name: load_HealthCanada_Opioid_Table
> ### Title: Obtain the latest Opioid data from Health Canada
> ### Aliases: load_HealthCanada_Opioid_Table
> 
> ### ** Examples
> 
>   HealthCanada_Opioid_Table <- load_HealthCanada_Opioid_Table(no_download = TRUE)
Error in open.connection(x, "rb") : 
  Timeout was reached: [www.canada.ca] Connection timeout after 10011 ms
Calls: load_HealthCanada_Opioid_Table -> <Anonymous> -> read_html.default
Execution halted
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Running examples in 'ordbetareg-Ex.R' failed
The error most likely occurred in:

> ### Name: pp_check_ordbeta
> ### Title: Accurate Posterior Predictive Plots for Ordbetareg Models
> ### Aliases: pp_check_ordbeta
> 
> ### ** Examples
> 
> 
> # need a fitted ordbetareg model
> 
> data("ord_fit_mean")
> 
> out_plots <- pp_check_ordbeta(ord_fit_mean)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': 'tcrossprod' is not an exported object from 'namespace:Matrix'
Error: Something went wrong (see the error message above). Perhaps you transformed numeric variables to factors or vice versa within the model formula? If yes, please convert your variables beforehand. Or did you use a grouping factor also for a different purpose? If yes, please make sure that its factor levels are correct also in the new data you may have provided.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'package_introduction.Rmd' using rmarkdown

Quitting from lines 197-209 [post_predict] (package_introduction.Rmd)
Error: processing vignette 'package_introduction.Rmd' failed with diagnostics:
Something went wrong (see the error message above). Perhaps you transformed numeric variables to factors or vice versa within the model formula? If yes, please convert your variables beforehand. Or did you use a grouping factor also for a different purpose? If yes, please make sure that its factor levels are correct also in the new data you may have provided.
--- failed re-building 'package_introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ordinalbayes.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'distsuml2':
  'partial'

Documented arguments not in \usage in documentation object 'distsumlp':
  'partial'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
Documented arguments not in \usage in documentation object 'dosepred':
  'w'

Documented arguments not in \usage in documentation object 'surv_dm_solver':
  'bw_optim'

Documented arguments not in \usage in documentation object 'surv_forward_solver':
  'Phit'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rcplex'
Rd files without \alias:
  'otp-package.Rd'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/OUwie.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'packagetracker.Rd':
  'packagetracker-package'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/packDAMipd.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Argument items with no description in Rd object 'joint_estimate':
  '\dots'
Argument items with no description in Rd object 'only_A_estimate':
  '\dots'
Argument items with no description in Rd object 'only_F_estimate':
  '\dots'
Argument items with no description in Rd object 'plot.Full_PAFit_result':
  '\dots'
Argument items with no description in Rd object 'plot.PAFit_net':
  '\dots'
Argument items with no description in Rd object 'plot.PAFit_result':
  '\dots'
Argument items with no description in Rd object 'plot.PA_result':
  '\dots'
Argument items with no description in Rd object 'print.CV_Result':
  '\dots'
Argument items with no description in Rd object 'print.CV_Data':
  '\dots'
Argument items with no description in Rd object 'print.Full_PAFit_result':
  '\dots'
Argument items with no description in Rd object 'print.PAFit_data':
  '\dots'
Argument items with no description in Rd object 'print.PAFit_net':
  '\dots'
Argument items with no description in Rd object 'print.PAFit_result':
  '\dots'
Argument items with no description in Rd object 'summary.CV_Data':
  '\dots'
Argument items with no description in Rd object 'summary.CV_Result':
  '\dots'
Argument items with no description in Rd object 'summary.Full_PAFit_result':
  '\dots'
Argument items with no description in Rd object 'summary.PAFit_data':
  '\dots'
Argument items with no description in Rd object 'summary.PAFit_net':
  '\dots'
Argument items with no description in Rd object 'summary.PAFit_result':
  '\dots'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    library  19.7Mb
Running examples in 'palaeoverse-Ex.R' failed
The error most likely occurred in:

> ### Name: phylo_check
> ### Title: Check phylogeny tip names
> ### Aliases: phylo_check
> 
> ### ** Examples
> 
> # track user par
> oldpar <- par(no.readonly = TRUE)
> #Read in example tree of ceratopsians from paleotree
> library(paleotree)
Loading required package: ape
Error: package or namespace load failed for 'paleotree':
 object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Package which this enhances but not available for checking: 'CorShrink'
Documented arguments not in \usage in documentation object 'other':
  'trial'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/paleotree.Rcheck/00install.out' for details.
Documented arguments not in \usage in documentation object 'dplyr_verbs':
  'funs' '.dots' 'keep_attributes'

Documented arguments not in \usage in documentation object 'nest_tdc':
  'vars' 'id'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'pamr-internal':
  'print.nsc' 'print.nsccv'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/PanelMatch.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Documented arguments not in \usage in documentation object 'getOption2':
  'envvar'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'expect_missing_argument':
  'message'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
--- re-building 'PartialNetwork_vignette.Rmd' using rmarkdown

Quitting from lines 747-749 [BayesLog0] (PartialNetwork_vignette.Rmd)
Error: processing vignette 'PartialNetwork_vignette.Rmd' failed with diagnostics:
cannot open the connection to 'https://github.com/ahoundetoungan/PartialNetwork/blob/master/datavignettes/out.logi.rda?raw=true'
--- failed re-building 'PartialNetwork_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'as_partition':
  '.partition_step'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'fixvar_of_red_mod':
  'data'

Documented arguments not in \usage in documentation object 'get_ndf':
  'data'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'vec_cast.partial_time':
  'vec_cast.partial_time'

S3 methods shown with full name in documentation object 'vec_cast.timespan':
  'vec_cast.timespan'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'help_console':
  'which'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'anomalize'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/patternize.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Argument items with no description in Rd object 'markbouts.acclist':
  'extreme'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      6.0Mb
    help   1.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    help   3.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   3.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   3.0Mb
S3 methods shown with full name in documentation object 'ped':
  'ped.markerNames'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'PBD-Ex.R' failed
The error most likely occurred in:

> ### Name: pbd_sim
> ### Title: Function to simulate the protracted speciation process
> ### Aliases: pbd_sim
> ### Keywords: models
> 
> ### ** Examples
>  pbd_sim(c(0.2,1,0.2,0.1,0.1),15) 
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'PBD_ML_demo.Rmd' using rmarkdown

Quitting from lines 34-49 [unnamed-chunk-3] (PBD_ML_demo.Rmd)
Error: processing vignette 'PBD_ML_demo.Rmd' failed with diagnostics:
object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'PBD_ML_demo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lib    2.8Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  d:/rtools43/x86_64-w64-mingw32.static.posix/include/coin/Clp_C_Interface.h:68:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/pcaL1.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   8.0Mb
GNU make is a SystemRequirements.
Objects in \usage without \alias in documentation object 'internals':
  'CumSum' 'myapply' 'makebreaks.ct' 'makebreaks.ic' 'pois.loglik'
  'icpch.loglik' 'convert.Surv' 'break.y' 'pois.fit' 'pch.fit.ct'
  'pch.fit.ic' 'newton' 'cleanlambda' 'predF.pch' 'predQ.pch' 'sim.pch'
  'build.splinex' 'predict.splinex' 'logLik.pch' 'nobs.pch' 'vcov.pch'
  'coef.pch' 'print.pch' 'summary.pch' 'print.summary.pch'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/pcmabc.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'getResponse':
  'model'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object 'ODACATH.estimate':
  'ODACAT.estimate'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'PythonInR'
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs    6.9Mb
    share  12.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/pdynmc.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/peacesciencer.Rcheck/00install.out' for details.
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'PoissonLoss':
  'count' 'seg.mean' 'weight'
Argument items with no description in Rd object 'getPath':
  'A'
Argument items with no description in Rd object 'PoissonLoss':
  'count' 'seg.mean' 'weight'
Argument items with no description in Rd object 'featureMatrixJoint':
  'profile.list'
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'PoissonLoss':
  'count' 'seg.mean' 'weight'
Argument items with no description in Rd object 'oracleModelComplexity':
  'bases' 'segments'
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'format.relation':
  'format.relation'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Missing or unexported object: 'Matrix::crossprod'
Running examples in 'pedigreeTools-Ex.R' failed
The error most likely occurred in:

> ### Name: getA
> ### Title: Additive relationship matrix
> ### Aliases: getA
> 
> ### ** Examples
> 
> ped <- pedigree(sire = c(NA, NA, 1,  1, 4, 5),
+                 dam =  c(NA, NA, 2, NA, 3, 2),
+                 label = 1:6)
> (A <- getA(ped))
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   2.2Mb
Package suggested but not available for checking: 'georob'
Invalid package aliases in Rd file 'pedSimulte-package.Rd':
  'pedSimulte-package'
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/PenCoxFrail.Rcheck/00install.out' for details.
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'lmres':
  '\dots'
Argument items with no description in Rd object 'simpleSlope':
  '\dots'
Argument items with no description in Rd object 'summary.lmres':
  '\dots'
Specified C++11: please drop specification unless essential
Running examples in 'perfectphyloR-Ex.R' failed
The error most likely occurred in:

> ### Name: RandIndexTest
> ### Title: Rand Index Test
> ### Aliases: RandIndexTest
> 
> ### ** Examples
> 
> 
> data(ex_hapMat_data)
> d1 <- reconstructPP(ex_hapMat_data, focalSNV = 1, minWindow = 1)
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'DMwR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dendextendRcpp'
Documented arguments not in \usage in documentation object 'allTrees':
  'dist'

Documented arguments not in \usage in documentation object 'getNode':
  'hc' 'pair'

Documented arguments not in \usage in documentation object 'switchEntries':
  'pair'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'perspective-package.Rd':
  'perspective-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/pez.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    application   4.9Mb
Invalid package aliases in Rd file '00_PH1XBAR-package.Rd':
  '00_PH1XBAR-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/phangorn.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'process_season':
  'd' 'options_season'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
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checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
    libs      1.0Mb
Auto-generated content requiring editing in Rd object 'phm-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'adaptive_smoothing':
  'smooth.limt' 'smooth.thershold'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::tcrossprod'
'LazyData' is specified without a 'data' directory
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/phyloregion.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/phylosem.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/PhySortR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/phytools.Rcheck/00install.out' for details.
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/piglet.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'pipegs.Rd':
  'pipegs-package'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Documented arguments not in \usage in documentation object 'TungUbRF':
  'feature_num_tree'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'pirouette-Ex.R' failed
The error most likely occurred in:

> ### Name: check_twinning_params
> ### Title: Checks if the argument is a valid twinning parameters structure.
> ### Aliases: check_twinning_params
> 
> ### ** Examples
> 
> check_twinning_params(create_twinning_params())
Error in value[[3L]](cond) : 
  'sim_twin_tree_fun' must be a function with one argument called 'true_phylogeny'
Calls: check_twinning_params ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'create_twin_tree.Rmd' using rmarkdown

Quitting from lines 20-24 [unnamed-chunk-1] (create_twin_tree.Rmd)
Error: processing vignette 'create_twin_tree.Rmd' failed with diagnostics:
package or namespace load failed for 'phangorn':
 object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'create_twin_tree.Rmd'

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

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

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

Quitting from lines 56-58 [unnamed-chunk-4] (partial_function_evaluation.Rmd)
Error: processing vignette 'partial_function_evaluation.Rmd' failed with diagnostics:
'sim_twin_tree_fun' must be a function with one argument called 'true_phylogeny'
--- failed re-building 'partial_function_evaluation.Rmd'

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

Quitting from lines 98-107 [unnamed-chunk-4] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'tutorial.Rmd'

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

Quitting from lines 48-49 [unnamed-chunk-3] (twinning.Rmd)
Error: processing vignette 'twinning.Rmd' failed with diagnostics:
'sim_twin_tree_fun' must be a function with one argument called 'true_phylogeny'
--- failed re-building 'twinning.Rmd'

SUMMARY: processing the following files failed:
  'create_twin_tree.Rmd' 'partial_function_evaluation.Rmd'
  'tutorial.Rmd' 'twinning.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'ggsubplot'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sanitize_latex.Rd:49: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'make_pgk_cache_subdir_for_all_relative_files':
  'relative_filenames'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
Documented arguments not in \usage in documentation object 'imports_env':
  'path'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    bin   8.6Mb
    doc   1.3Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/PlackettLuce.Rcheck/00install.out' for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Package suggested but not available for checking: 'RStoolbox'
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::tcrossprod'
Running examples in 'plantTracker-Ex.R' failed
The error most likely occurred in:

> ### Name: aggregateByGenet
> ### Title: aggregateByGenet
> ### Aliases: aggregateByGenet
> 
> ### ** Examples
> 
> dat <- grasslandData[grasslandData$Site == c("AZ") &
+  grasslandData$Species %in% c("Bouteloua rothrockii", "Calliandra eriophylla" ),]
> names(dat)[1] <- "speciesName"
> inv <- grasslandInventory[unique(dat$Quad)]
> outDat <- trackSpp(dat = dat,
+  inv = inv,
+  dorm = 1,
+  buff = .05,
+  buffGenet = 0.005,
+  clonal = data.frame("Species" = unique(dat$speciesName),
+  "clonal" = c(TRUE,FALSE)),
+  species = "speciesName",
+  aggByGenet = FALSE
+  )
Site: AZ

-- Quadrat: SG2

Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/PlasmaMutationDetector2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/PlasmaMutationDetector.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in 'pliman-Ex.R' failed
The error most likely occurred in:

> ### Name: efourier
> ### Title: Elliptical Fourier Analysis
> ### Aliases: efourier
> 
> ### ** Examples
> 
> library(pliman)
> leaf1 <- contours[[4]]
> plot_polygon(leaf1)
> 
> #### default options
> # 10 harmonics (default)
> # without alignment
> 
> ef <- efourier(leaf1)
> efourier_coefs(ef)
           an           bn          cn           dn
1  21.1298663 -382.7540180 -364.126202 -21.29189747
2   1.6804167  151.6255507  -40.467153  10.80476561
3   4.3779839   -0.9870311 -129.212508   3.20445130
4  -3.1329537  -46.3028113  -26.380285  -4.12257511
5  -1.6548827    3.6997248   19.343685  -3.32106033
6   4.9296483   39.2656639  -15.461424   0.48631684
7   1.2043295    0.5415148  -15.556049   0.96104147
8   0.5959547  -13.0422412  -18.885184   1.42268431
9  -0.8187422    3.9795071   -4.368973   0.04457129
10 -0.3849895   -5.7461417   -2.553430  -1.11528942
> 
> # object is aligned along the major caliper with `poly_align()`
> # object is centered on the origin with `poly_center()`
> # using a list of object coordinates
> ef2 <- efourier(contours, align = TRUE, center = TRUE)
Error in eval(substitute(list(...)), `_data`, parent.frame()) : 
  object 'X1' not found
Calls: efourier ... transform.default -> transform.data.frame -> eval -> eval
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in 'PLMIX-Ex.R' failed
The error most likely occurred in:

> ### Name: as.top_ordering
> ### Title: Coercion into top-ordering datasets
> ### Aliases: as.top_ordering
> 
> ### ** Examples
> 
> 
> ## Coerce an object of class 'rankings' into an object of class 'top_ordering'
> library(PlackettLuce)
Error: package or namespace load failed for 'PlackettLuce':
 object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'plsgenomics-deprecated.Rd':
  'plsgenomics-deprecated-package'
Invalid package aliases in Rd file 'plsgenomics-internal.Rd':
  'plsgenomics-internal-package'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'eval.quoted':
  'expr'

Documented arguments not in \usage in documentation object 'indexed_df':
  'env'

Documented arguments not in \usage in documentation object 'list_to_dataframe':
  'idname'

Documented arguments not in \usage in documentation object 'split_indices':
  'index'

Documented arguments not in \usage in documentation object 'split_labels':
  'list' 'whether'

Documented arguments not in \usage in documentation object 'tryapply':
  'f'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/pmc.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'sample_store':
  'subjects_ids'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Objects in \usage without \alias in documentation object 'PMwR-internal':
  '.timestamp<-'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
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checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'pollimetrydata'
Running examples in 'pollimetry-Ex.R' failed
The error most likely occurred in:

> ### Name: bodysize
> ### Title: Converts the intertegular distance (IT) and co-variates to body
> ###   size in dry weight (mg) for bees or hoverflies.
> ### Aliases: bodysize
> 
> ### ** Examples
> 
> example=cbind.data.frame(IT=c(1.3,2.3),
+                          Sex=c("Female","Male"), 
+                          Subfamily=c("Syrphinae","Eristalinae"),
+                          Region=c("Australasia","Europe"),
+                          Species=c("Sphaerophoria_macrogaster","Myathropa_florea"))
> bodysize(x=example,taxa="hov",type="taxo")
Loading required namespace: pollimetrydata
Failed with error:  'there is no package called 'pollimetrydata''
Downloading data from: https://github.com/liamkendall/pollimetrydata/raw/master/data/hov_tax_mod.rdata 

SHA-1 hash of the downloaded data file is:
8fabe989dfed6c91d8e5834ad224ff4865b76b7f
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': 'tcrossprod' is not an exported object from 'namespace:Matrix'
Error: Something went wrong (see the error message above). Perhaps you transformed numeric variables to factors or vice versa within the model formula? If yes, please convert your variables beforehand. Or did you use a grouping factor also for a different purpose? If yes, please make sure that its factor levels are correct also in the new data you may have provided.
Execution halted
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'gpclib'
Unknown package 'gpclib' in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
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installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   1.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      1.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data      2.7Mb
    extdata   3.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
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Documented arguments not in \usage in documentation object 'initialize,genclone-method':
  'gen' 'loc' 'treatOther' 'quiet'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 
> ### ** Examples
> 
>  ff <- function(x = 1, null_return = "hello"){
+    return_if_null(x, null_return)
+    x
+  }
>  ff()
[1] 1
>  ff(NULL)
[1] "hello"
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  0.67 0.08 0.75 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Problems with news in 'NEWS.md':
No news entries found.
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checkRd: (-1) tradelist-class.Rd:91: Escaped LaTeX specials: \$
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/postGGIR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
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Unknown package 'advclust' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object 'ppmlasso-internal':
  'spatRes'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
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installed size is 11.0Mb
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    doc  10.4Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/PRECAST.Rcheck/00install.out' for details.
Documented arguments not in \usage in documentation object 'local_test_setup':
  'use_precommmit'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata  11.6Mb
Package which this enhances but not available for checking: 'ffbase'
Unknown package 'ffbase' in Rd xrefs
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::tcrossprod'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    extdata   9.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinyApp   5.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.3Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    4.7Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Missing or unexported objects:
  'Matrix::crossprod' 'Matrix::tcrossprod'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
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    htmlwidgets   2.5Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ProFAST.Rcheck/00install.out' for details.
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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Documented arguments not in \usage in documentation object 'validate_inputs':
  'required_vars'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.0Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cin'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'bitAND':
  'a' 'b'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rdt'
Documented arguments not in \usage in documentation object '.marxan_data_reader':
  'parameter'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/prWarp.Rcheck/00install.out' for details.
Invalid package aliases in Rd file 'granova-package.Rd':
  'granova-package'
Documented arguments not in \usage in documentation object 'estimateDeltaLOH.PairedPSCBS':
  'scale'

Documented arguments not in \usage in documentation object 'getLocusData.AbstractCBS':
  'splitters'

Documented arguments not in \usage in documentation object 'getSegments.AbstractCBS':
  'simplify' 'splitters'

Documented arguments not in \usage in documentation object 'mergeTwoSegments.AbstractCBS':
  'left' 'update' 'verbose'

Documented arguments not in \usage in documentation object 'plotTracks.PairedPSCBS':
  'x' 'tracks' 'scatter' 'calls' 'pch' 'col' 'cex' 'changepoints'
  'grid' 'quantiles' 'xlim' 'Clim' 'Blim' 'xScale' 'add' 'subplots'
  'verbose'

Documented arguments not in \usage in documentation object 'updateMeansTogether.AbstractCBS':
  'idxList' 'verbose'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'kepner_robinson_test_internal':
  'group' 'alternative' 'trend'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'pspline.sample.scalars':
  'time'

Documented arguments not in \usage in documentation object 'pspline.sample.timeseries':
  'time'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  arch/windows/process_handles.h:100:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  arch/windows/process_handles.c:23:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/ps.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/psSubpathway.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file '00.psych-package.Rd':
  '00.psych-package'
Documented arguments not in \usage in documentation object 'GetFitHReg':
  'z'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Invalid package aliases in Rd file 'package-ptf.Rd':
  'package-ptf-package'
Documented arguments not in \usage in documentation object 'assert_correct_attributes':
  'expected_colnames'

Documented arguments not in \usage in documentation object 'geopath_to_tibble':
  'route'

Documented arguments not in \usage in documentation object 'run_to_tibble':
  'route'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/pulseTD.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'PVAClone-package.Rd':
  'PVA-package' 'pva-package' 'Pva-package'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/PWIR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
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installed size is  7.3Mb
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Documented arguments not in \usage in documentation object 'http_was_redirected':
  'response'

Documented arguments not in \usage in documentation object 'permutations':
  'nset'

Documented arguments not in \usage in documentation object 'pxweb_split_query':
  'pxweb_metadata'

Documented arguments not in \usage in documentation object 'split_dimensions_left_right':
  'pxq'

Documented arguments not in \usage in documentation object 'str_pad':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Documented arguments not in \usage in documentation object 'lagm':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'get_names_MV':
  'path_matrix'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object 'internals':
  'expit' 'logit' 'pmax0' 'num.fun' 'format.perc' 'Ltau' 'minabs'
  'invJ' 'tensorX' 'buildTau' 'callwtau' 'callQ' 'start.Qest'
  'start.Qest.family' 'rq.fit.br2' 'Qest.sgs.internal'
  'Qest.gs.internal' 'Qest.gs' 'Qest.newton' 'Qlm.bfun' 'start.Qlm'
  'scalevars.Qlm' 'descalecoef.Qlm' 'Qlm.sgs.internal'
  'Qlm.gs.internal' 'Qlm.gs' 'Qlm.newton' 'plfcox' 'scalevars.Qcoxph'
  'descalecoef.Qcoxph' 'check.singularities' 'starting.points.Qcox'
  'adjust.coef' 'agsurv.Qcoxph' 'coxsurv.fit.Qcoxph' 'seg.lm.fit1' 'gs'
  'myg' 'dlist' 'omega' 'choose_eps' 'derQtheta' 'der2Qtheta' 'intA'
  'findp' 'findAp' 'A_beta_fun' 'A_gamma_fun' 'A_beta_beta_fun'
  'A_gamma_gamma_mix_fun' 'A_gamma_gamma_fun' 'A_beta_gamma_fun'
  'coxBB' 'derQtheta.gamma' 'der2Qtheta.gamma' 'findAp.gamma'
  'QestGamma.ee.u' 'QestGamma.ee.c' 'QestGamma.ee.ct' 'tau.pois'
  'ppoisC' 'dpoisC' 'qpoisC.955' 'qpoisC.me' 'qpoisC.bisec' 'qpoisC'
  'derQtheta.pois' 'der2Qtheta.pois' 'findp.pois' 'findAp.pois'
  'QestPois.ee.u' 'QestUnif.ee.u' 'QestNorm.ee.u' 'QestNorm.ee.c'
  'QestNorm.ee.ct' 'Qest.ee.u' 'Qest.ee.c' 'Qest.ee.ct' 'QCox.ee.c'
  'QCox.ee.ct' 'Qlm.ee.u' 'Qest.covar' 'Qcox.covar' 'Qlm.covar' 'Loss'
  'coxLoss' 'qlmLoss'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'internals':
  'format.perc'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/qgcompint.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/qgcomp.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spDataLarge'
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'ad.simudata':
  'SimuNum'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in documentation object 'internals':
  'Q' 'funQ1' 'check.fun' 'boot' 'predBeta' 'grad3' 'grad2' 'num.int'
  'integr' 'bisec' 'Bfun' 'bfun' 'funGrad' 'Fun' 'armijo' 'check.in.2'
  'check.out.2' 'piqr.newton' 'piqr.ee' 'pciqr.ee' 'pctiqr.ee'
  'plotCoef' 'nonzeroCoef' 'cov.theta.2' 'plot.piqr2'
  'divide.et.impera.2' 'print.niqr' 'print.summary.niqr' 'print.piqr'
  'print.summary.piqr' 'terms.piqr' 'coef.piqr' 'model.matrix.piqr'
  'nobs.piqr'
Assignments in \usage in documentation object 'internals':
  start.theta.niqr <- function(fun, x0, X, y, control = list()) piqr.internal(mf, 
      cl, formula.p, tol = 1e-06, maxit = 100, s, segno = 1, lambda = 0, 
      check = FALSE, A, st.theta = FALSE, theta0)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'internals':
  'plot.piqr2'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Objects in \usage without \alias in documentation object 'internals':
  'check.in.iqr' 'check.in0.iqrL' 'check.in.iqrL' 'check.out'
  'start.iqr' 'start.iqrL' 'ctiqr.internal' 'iqrL.internal' 'iqrL.fit'
  'iqr.ee' 'ciqr.ee' 'ctiqr.ee' 'iobjfun' 'iobjfun.ct' 'cov.fun.iqr'
  'iqrL.ee' 'cov.fun.iqrL' 'iqr.newton' 'divide.et.impera'
  'iqrL.newton' 'pmax0' 'maxind' 'num.fun' 'make.bfun' 'apply_bfun'
  'p.bisec' 'p.bisec.internal' 'slp.basis' 'is.slp' 'safesolve'
  'iqr.waldtest' 'extract.p' 'pred.beta' 'km' 'alpha' 'test.unif.ct'
  'findagoodestimator' 'quickpred' 'trans' 'alpha.bisec'
  'alpha.bisec.out' 'ks' 'print.iqr' 'print.summary.iqr' 'terms.iqr'
  'model.matrix.iqr' 'vcov.iqr' 'nobs.iqr' 'predict.iqrL.internal'
  'print.iqrL' 'print.summary.iqrL' 'terms.iqrL' 'model.matrix.iqrL'
  'vcov.iqrL' 'nobs.iqrL' 'qc.penalty' 'fixqc' 'print.qc.iqr'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'internals':
  'predict.iqrL.internal'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
checkRd: (-1) NEWS.Rd:15: Escaped LaTeX specials: \&
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      2.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/qtlnet.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'mmer_adapted':
  'void'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'export_responses_filedownload':
  'requestID'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Missing or unexported object: 'Matrix::crossprod'
Documented arguments not in \usage in documentation object 'convert-wrappers':
  '...'

Documented arguments not in \usage in documentation object 'corpus-class':
  'if'

Documented arguments not in \usage in documentation object 'dfm-class':
  'drop_docid'

Documented arguments not in \usage in documentation object 'dictionary2-class':
  'object'

Documented arguments not in \usage in documentation object 'matrix2fcm':
  'slots'

Documented arguments not in \usage in documentation object 'meta_system':
  'source'

Documented arguments not in \usage in documentation object 'search_index':
  'regex'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'quanteda-Ex.R' failed
The error most likely occurred in:

> ### Name: dfm_compress
> ### Title: Recombine a dfm or fcm by combining identical dimension elements
> ### Aliases: dfm_compress fcm_compress
> 
> ### ** Examples
> 
> # dfm_compress examples
> dfmat <- rbind(dfm(tokens(c("b A A", "C C a b B")), tolower = FALSE),
+                dfm(tokens("A C C C C C"), tolower = FALSE))
> colnames(dfmat) <- char_tolower(featnames(dfmat))
> dfmat
Document-feature matrix of: 3 documents, 5 features (46.67% sparse) and 0 docvars.
         features
docs      b a c a b
  text1.1 1 2 0 0 0
  text2.1 1 0 2 1 1
  text1.2 0 1 5 0 0
> dfm_compress(dfmat, margin = "documents")
Document-feature matrix of: 2 documents, 5 features (30.00% sparse) and 0 docvars.
       features
docs    b a c a b
  text1 1 3 5 0 0
  text2 1 0 2 1 1
> dfm_compress(dfmat, margin = "features")
Document-feature matrix of: 3 documents, 3 features (22.22% sparse) and 0 docvars.
         features
docs      b a c
  text1.1 1 2 0
  text2.1 2 1 2
  text1.2 0 1 5
> dfm_compress(dfmat)
Document-feature matrix of: 2 documents, 3 features (0.00% sparse) and 0 docvars.
       features
docs    b a c
  text1 1 3 5
  text2 2 1 2
> 
> # no effect if no compression needed
> dfmatsubset <- dfm(tokens(data_corpus_inaugural[1:5]))
> dim(dfmatsubset)
[1]    5 1948
> dim(dfm_compress(dfmatsubset))
[1]    5 1948
> 
> # compress an fcm
> fcmat1 <- fcm(tokens("A D a C E a d F e B A C E D"),
+              context = "window", window = 3)
> ## this will produce an error:
> # fcm_compress(fcmat1)
> 
> txt <- c("The fox JUMPED over the dog.",
+          "The dog jumped over the fox.")
> toks <- tokens(txt, remove_punct = TRUE)
> fcmat2 <- fcm(toks, context = "document")
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'quickstart.Rmd' using rmarkdown

Quitting from lines 492-497 [unnamed-chunk-42] (quickstart.Rmd)
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
'crossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'quickstart.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
Missing or unexported object: 'Matrix::tcrossprod'
Running examples in 'quanteda.textmodels-Ex.R' failed
The error most likely occurred in:

> ### Name: predict.textmodel_nb
> ### Title: Prediction from a fitted textmodel_nb object
> ### Aliases: predict.textmodel_nb coef.textmodel_nb
> ###   coefficients.textmodel_nb
> ### Keywords: internal textmodel
> 
> ### ** Examples
> 
> # application to LBG (2003) example data
> (tmod <- textmodel_nb(quanteda::data_dfm_lbgexample, y = c("A", "A", "B", "C", "C", NA)))

Call:
textmodel_nb.dfm(x = quanteda::data_dfm_lbgexample, y = c("A", 
    "A", "B", "C", "C", NA))

 Distribution: multinomial ; priors: 0.3333333 0.3333333 0.3333333 ; smoothing value: 1 ; 5 training documents;  fitted features. 
> predict(tmod)
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'textmodel_performance.Rmd' using rmarkdown

Quitting from lines 53-60 [unnamed-chunk-4] (textmodel_performance.Rmd)
Error: processing vignette 'textmodel_performance.Rmd' failed with diagnostics:
'tcrossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'textmodel_performance.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in documentation object 'wordcloud_comparison':
  'random.color' 'ordered.colors'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'quanteda.textplots-Ex.R' failed
The error most likely occurred in:

> ### Name: textplot_network
> ### Title: Plot a network of feature co-occurrences
> ### Aliases: textplot_network as.network.fcm as.igraph.fcm
> ### Keywords: textplot
> 
> ### ** Examples
> 
> set.seed(100)
> library("quanteda")
Package version: 3.3.1
Unicode version: 13.0
ICU version: 69.1
Parallel computing: 2 of 96 threads used.
See https://quanteda.io for tutorials and examples.
> toks <- data_char_ukimmig2010 %>%
+     tokens(remove_punct = TRUE) %>%
+     tokens_tolower() %>%
+     tokens_remove(pattern = stopwords("english"), padding = FALSE)
> fcmat <- fcm(toks, context = "window", tri = FALSE)
> feat <- names(topfeatures(fcmat, 30))
> fcm_select(fcmat, pattern = feat) %>%
+     textplot_network(min_freq = 0.5)
> fcm_select(fcmat, pattern = feat) %>%
+     textplot_network(min_freq = 0.8)
> fcm_select(fcmat, pattern = feat) %>%
+     textplot_network(min_freq = 0.8, vertex_labelcolor = rep(c('gray40', NA), 15))
> fcm_select(fcmat, pattern = feat) %>%
+     textplot_network(vertex_labelsize = 10)
> fcm_30 <- fcm_select(fcmat, pattern = feat)
> textplot_network(fcm_30,
+                  vertex_labelsize = Matrix::rowSums(fcm_30) / min(Matrix::rowSums(fcm_30)))
> # Vector inputs to vertex_labelsize can be scaled if too small / large
> textplot_network(fcm_30,
+                  vertex_labelsize = 1.5 * Matrix::rowSums(fcm_30) /
+                                     min(Matrix::rowSums(fcm_30)))
> 
> # as.igraph
> if (requireNamespace("igraph", quietly = TRUE)) {
+     txt <- c("a a a b b c", "a a c e", "a c e f g")
+     mat <- fcm(txt)
+     as.igraph(mat, min_freq = 1, omit_isolated = FALSE)
+ }
Warning: 'fcm.character()' is deprecated. Use 'tokens()' or 'dfm()' first.
Warning: 'fcm.corpus()' is deprecated. Use 'tokens()' or 'dfm()' first.
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Aliases: query_uniprot
> 
> ### ** Examples
> 
> # Get the UniProt entries of all proteins encoded by gene Pik3r1
> ids <- c("P22682", "P47941")
> query = list("accession_id" = ids)
> df <-  query_uniprot(query = query)
> head(df)
   Entry Entry Name Gene Names Organism (ID) Reviewed
2 P22682  CBL_MOUSE        Cbl         10090 reviewed
3 P47941 CRKL_MOUSE Crkl Crkol         10090 reviewed
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  0.31 0.04 0.77 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Auto-generated content requiring editing in Rd object 'quhomology-package':
  \details: '...o use the package, including the most important functions ~~'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'fastshp'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    shiny_app   1.4Mb
Invalid package aliases in Rd file 'qut-package.Rd':
  'QUT-package'
Specified C++11: please drop specification unless essential
checkRd: (-1) qwraps2.Rd:73: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::crossprod'
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(r2glmm)
  > 
  > test_check("r2glmm")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_R2.R:14:1'): (code run outside of `test_that()`) ───────────────
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'a' in selecting a method for function 'solve': 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─r2glmm::r2beta(model = lmemod, method = "sgv", partial = T) at test_R2.R:14:0
   2. ├─r2glmm:::r2beta.lme(model = lmemod, method = "sgv", partial = T)
   3. │ └─base::lapply(...)
   4. │   └─r2glmm (local) FUN(X[[i]], ...)
   5. │     └─Matrix::solve(Matrix::crossprod(Xmt))
   6. └─base::.handleSimpleError(...)
   7.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   5.0Mb
Package suggested but not available for checking: 'RDCOMClient'
'library' or 'require' call to 'RDCOMClient' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'BRugs'
Documented arguments not in \usage in documentation object 'bugs.inits':
  'inits.file'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/rabhit.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs          2.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object '.armaRidgeP':
  'alpha'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rainette)
  
  Attaching package: 'rainette'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  > 
  > test_check("rainette")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 183 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_plots.R:6:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_rainette1.R:27:5'): order_docs ─────────────────────────────────
  Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─quanteda.textmodels::textmodel_ca(mini_dfm) at test_rainette1.R:27:4
   2. └─quanteda.textmodels:::textmodel_ca.dfm(mini_dfm)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 183 ]
  Deleting unused snapshots:
  • plots/base-rainette-plot-measure-docprop.svg
  • plots/base-rainette-plot-measure-frequency.svg
  • plots/base-rainette-plot-measure-lr.svg
  • plots/base-rainette-plot-with-free-scales.svg
  • plots/base-rainette-plot-with-k-and-without-negative.svg
  • plots/base-rainette-plot-with-k-n-terms-and-font-size.svg
  • plots/base-rainette-plot.svg
  • plots/base-rainette2-plot-measure-docprop.svg
  • plots/base-rainette2-plot-measure-frequency.svg
  • plots/base-rainette2-plot-measure-lr.svg
  • plots/base-rainette2-plot-with-complete-groups.svg
  • plots/base-rainette2-plot-with-free-scales.svg
  • plots/base-rainette2-plot-with-k-5.svg
  • plots/base-rainette2-plot-with-k-and-without-negative.svg
  • plots/base-rainette2-plot-with-k-n-terms-and-font-size.svg
  • plots/base-rainette2-plot.svg
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets  10.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   6.8Mb
Documented arguments not in \usage in documentation object 'print.ramchoiceRevealAtte':
  'object'

Documented arguments not in \usage in documentation object 'print.ramchoiceRevealPref':
  'object'

Documented arguments not in \usage in documentation object 'print.ramchoiceRevealPrefModel':
  'object'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/randnet.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Invalid package aliases in Rd file 'randtests-package.Rd':
  'randomtests-package'
Package suggested but not available for checking: 'googlesheets'
Missing or unexported objects:
  'Matrix::crossprod' 'Matrix::tcrossprod'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'get_parameters':
  'parameters_def'

Documented arguments not in \usage in documentation object 'print.rapi_api':
  '...further'

Documented arguments not in \usage in documentation object 'print.rapi_operation':
  '...further'

Documented arguments not in \usage in documentation object 'print.rapi_schema_function':
  '...further'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'RApiDatetime-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '# Optional simple examples of the most important functions'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RapidoPGS.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/rapidphylo.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      1.4Mb
Objects in \usage without \alias in documentation object 'cache':
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  '\S4method{cache}{RapData,character,missing}'
  '\S4method{cache}{RapResults,character,ANY}'
  '\S4method{cache}{RapResults,character,missing}'

Objects in \usage without \alias in documentation object 'is.cached':
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  '\S4method{is.cached}{RapResults,character}'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Documented arguments not in \usage in documentation object 'mpaRaoS':
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Objects in \usage without \alias in documentation object 'paRaoP':
  'paRaoS'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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    libs   1.4Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ratematrix.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Documented arguments not in \usage in documentation object 'convert_to_native_raster':
  'ncol' 'nrow'

Documented arguments not in \usage in documentation object 'pad_to_fit':
  'heightmap' 'pad'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'onb_from_w':
  'v'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'init_time':
  'verbose' 'message'

Documented arguments not in \usage in documentation object 'print_time':
  'message'

Documented arguments not in \usage in documentation object 'process_point_series_1d':
  'points'

Documented arguments not in \usage in documentation object 'process_point_series_2d':
  'points'

Documented arguments not in \usage in documentation object 'tween':
  'type'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'gen_fractal_perlin':
  'image'

Documented arguments not in \usage in documentation object 'generate_base_shape':
  'image'

Documented arguments not in \usage in documentation object 'generate_cloud_layer':
  'image'

Documented arguments not in \usage in documentation object 'make_base_triangulated':
  'zscale'

Documented arguments not in \usage in documentation object 'raymarch_cloud_layer':
  'image'

Documented arguments not in \usage in documentation object 'render_snapshot_software':
  'ground_size'

Documented arguments not in \usage in documentation object 'transform_into_heightmap_coords':
  'image'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'generate_toon_outline':
  'angle' 'order_rotation'

Documented arguments not in \usage in documentation object 'init_time':
  'verbose' 'message'

Documented arguments not in \usage in documentation object 'merge_scene':
  'scene'

Documented arguments not in \usage in documentation object 'print_time':
  'message'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'Min_Max_Inverse_Scale_Vec':
  'mat'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'export.default':
  'export.default'

S3 methods shown with full name in documentation object 'export.listpoly':
  'export.listpoly'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    cont  24.2Mb
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'makeTitle':
  'string:' 'length:' 'prefix.length:' 'char:'

Documented arguments not in \usage in documentation object 'messageConsole':
  'message:'

Documented arguments not in \usage in documentation object 'tkEmptyLine':
  'tk.object:' 'row:'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Invalid package aliases in Rd file 'RcmdrPlugin.coin-package.Rd':
  'RcmdrcoinPlugin-package'
S3 methods shown with full name in documentation object 'editDataset.design':
  'editDataset.design'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'Rcmdr.HH-package.Rd':
  'Rcmdr.HH-package'
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'RcmdrPlugin.SCDA-package.Rd':
  'RcmdrSCDAPlugin-package'
Argument items with no description in Rd object 'aovreml':
  'formula' 'data' 'Lconfint' 'REML' '\dots'
Argument items with no description in Rd object 'aovremm':
  'formula' 'data' '\dots'
Argument items with no description in Rd object 'characRV':
  'D' 'charact' 'moment' 'cmoment'
Argument items with no description in Rd object 'plotRegions':
  'D' 'add' 'regions' 'col' 'legend' 'legend.pos' 'to.draw.arg'
  'verticals' 'ngrid' 'cex.points' 'mfColRow' 'lwd' '\dots'
Package suggested but not available for checking: 'ROpenOffice'
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   4.5Mb
    po    2.4Mb
Package suggested but not available for checking: 'conics'
installed size is  7.5Mb
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    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RCPA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Rcplex.Rcheck/00install.out' for details.
Auto-generated content requiring editing in Rd object 'RcppAnnoy-package':
  \examples: '# Optional simple examples of the most important functions'
Specified C++11: please drop specification unless essential
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
    libs      1.2Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.2Mb
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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Invalid package aliases in Rd file 'RcppHnsw-package.Rd':
  'RcppHnsw-package'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.1Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.3Mb
installed size is  8.0Mb
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    include        2.0Mb
    jsonexamples   3.8Mb
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NEWS.Rd:46: First argument to \href must be verbatim URL
problem found in 'NEWS.Rd'
Auto-generated content requiring editing in Rd object 'RcppSpdlog-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '## Optional simple examples of the most important functions ...'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'RCT-Ex.R' failed
The error most likely occurred in:

> ### Name: impact_eval
> ### Title: Impact Evaluation of Treatment Effects
> ### Aliases: impact_eval
> 
> ### ** Examples
> 
> data <- data.frame(y_1 = rnorm(n = 100, mean = 100, sd = 15), 
+                   y_2 = rnorm(n = 100, mean = 8, sd = 2), 
+                   treat = rep(c(0,1,2,3), each = 25), 
+                   heterogenous_var1 = rep(c("X_Q1", "X_Q2", "X_Q3", "X_Q4"), times = 25),
+                   cluster_var1 = rep(c(1:5), times = 20), 
+                   fixed_effect_var1 = rep(c(1,2), times = 50),
+                   control_var1 = rnorm(n = 100, mean = 20, sd = 1))
> 
> evaluation<-impact_eval(data = data, 
+                        endogenous_vars = c("y_1", "y_2"), 
+                        treatment = "treat", 
+                        heterogenous_vars = c("heterogenous_var1"), 
+                        cluster_vars = "cluster_var1", fixed_effect_vars = c("fixed_effect_var1"), 
+                        control_vars = c("control_var1"))
Error in `purrr::map()`:
ℹ In index: 1.
Caused by error:
! object 'crossprod' is not exported by 'namespace:Matrix'
Backtrace:
     ▆
  1. ├─RCT::impact_eval(...)
  2. │ └─purrr::map(...)
  3. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  4. │     ├─purrr:::with_indexed_errors(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     ├─purrr:::call_with_cleanup(...)
  7. │     └─RCT (local) .f(.x[[i]], ...)
  8. │       └─lfe::felm(stats::as.formula(.), data = data) %>% ...
  9. ├─broom::tidy(.)
 10. ├─base::loadNamespace(x)
 11. │ └─base::namespaceImportFrom(...)
 12. │   └─base::importIntoEnv(impenv, impnames, ns, impvars)
 13. │     └─base::stop(...)
 14. └─base::.handleSimpleError(...)
 15.   └─purrr (local) h(simpleError(msg, call))
 16.     └─cli::cli_abort(...)
 17.       └─rlang::abort(...)
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(RCT)
  > 
  > test_check("RCT")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 73 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_impact_eval.R:16:1'): (code run outside of `test_that()`) ──────
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::map(formulas, ~lfe::felm(stats::as.formula(.), data = data) %>% 
      broom::tidy(.))`: ℹ In index: 1.
  Caused by error:
  ! object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─RCT::impact_eval(...) at test_impact_eval.R:16:0
    2. │ └─purrr::map(...)
    3. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
    4. │     ├─purrr:::with_indexed_errors(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     ├─purrr:::call_with_cleanup(...)
    7. │     └─RCT (local) .f(.x[[i]], ...)
    8. │       └─lfe::felm(stats::as.formula(.), data = data) %>% ...
    9. ├─broom::tidy(.)
   10. ├─base::loadNamespace(x)
   11. │ └─base::namespaceImportFrom(...)
   12. │   └─base::importIntoEnv(impenv, impnames, ns, impvars)
   13. │     └─base::stop(...)
   14. └─base::.handleSimpleError(...)
   15.   └─purrr (local) h(simpleError(msg, call))
   16.     └─cli::cli_abort(...)
   17.       └─rlang::abort(...)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 73 ]
  Error: Test failures
  Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
GNU make is a SystemRequirements.
Invalid package aliases in Rd file 'Rd2markdown-package.Rd':
  'Rd2markdown-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'h_opt_density_res':
  'x' 'dgp_F1' 'dgp_Fp1' 'f_low' 'f_up'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'devAll'
Documented arguments not in \usage in documentation object 'favicon':
  'file'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'rdoc_options.Rd':
  'rdoc_options-package'
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'RDocumentation-package':
  \details: '...o use the package, including the most important functions ~~'
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: virustotal_cat
> ### Title: Get Category from Virustotal
> ### Aliases: virustotal_cat
> 
> ### ** Examples
> 
> ## Not run: 
> ##D virustotal_cat("http://www.google.com")
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  5.19 0.6 5.79 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.5Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) re2_syntax.Rd:539: Escaped LaTeX specials: \_
Package suggested but not available for checking: 'dataui'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object '.readAcquFile':
  'file'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'readmnist-package':
  \details: '...the package, including the most important ~~ ~~ functions ~~'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'add_docid':
  'impute_types'

Documented arguments not in \usage in documentation object 'texts':
  'spacer'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'rearrr_fn_':
  'overwrite'

Documented arguments not in \usage in documentation object 'rev_windows_rearranger_':
  'keep_windows'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/recluster.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
--- finished re-building 'Introduction.Rmd'

--- re-building 'step00_prep.Rmd' using rmarkdown
--- finished re-building 'step00_prep.Rmd'

--- re-building 'step01_loading.Rmd' using rmarkdown
--- finished re-building 'step01_loading.Rmd'

--- re-building 'step02_initial_cluster.Rmd' using rmarkdown
--- finished re-building 'step02_initial_cluster.Rmd'

--- re-building 'step03_refinement.Rmd' using rmarkdown
--- finished re-building 'step03_refinement.Rmd'

--- re-building 'step04_manual_tweak.Rmd' using rmarkdown
--- re-building 'step05_visualization_export.Rmd' using rmarkdown
--- finished re-building 'step05_visualization_export.Rmd'

SUMMARY: processing the following file failed:
  'step04_manual_tweak.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
Auto-generated content requiring editing in Rd object 'recom-package':
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'EDM.Rd':
  'EDM-package'
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'RED.Rd':
  'RED-package'
Auto-generated content requiring editing in Rd object 'referenceIntervals-package':
  \references: '~~ Literature or other references for background information ~~'
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/refund.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/refund.shiny.Rcheck/00install.out' for details.
Found export directive that requires package 'methods':
  'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'Estep':
  'adaptive_quad'

Documented arguments not in \usage in documentation object 'd_bernoulli':
  'pred.data' 'num.quad'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.3Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RegSDC.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'short_intro.Rmd' using knitr

Quitting from lines 45-46 [unnamed-chunk-3] (short_intro.Rmd)
Error: processing vignette 'short_intro.Rmd' failed with diagnostics:
objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
--- failed re-building 'short_intro.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) calc.relimp.Rd:41: Escaped LaTeX specials: \~
checkRd: (-1) classesmethods.relaimpo.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) classesmethods.relaimpo.Rd:104: Escaped LaTeX specials: \$
checkRd: (-1) mianalyze.relimp.Rd:69: Escaped LaTeX specials: \~
checkRd: (-1) mianalyze.relimp.Rd:73: Escaped LaTeX specials: \~
checkRd: (-1) relimplm-class.Rd:63: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbootMI-class.Rd:121: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbooteval-class.Rd:146: Escaped LaTeX specials: \$
Package which this enhances but not available for checking: 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:42: Escaped LaTeX specials: \$
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/REndo.Rcheck/00install.out' for details.
Invalid package aliases in Rd file 'Renvlp.Rd':
  'Revnlp-package'
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'REPPlab-package.Rd':
  'R/EPP-lab-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in 'reReg-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.reReg
> ### Title: Plot the Baseline Cumulative Rate Function and the Baseline
> ###   Cumulative Hazard Function
> ### Aliases: plot.reReg
> ### Keywords: Plots
> 
> ### ** Examples
> 
> data(simDat)
> fm <- Recur(t.start %to% t.stop, id, event, status) ~ x1 + x2
> 
> fit <- reReg(fm, data = simDat, B = 0)
> plot(fit)
> plot(fit, xlab = "Time (days)", smooth = TRUE)
> 
> ## Predicted cumulative rate and hazard given covariates
> newdata <- expand.grid(x1 = 0:1, x2 = mean(simDat$x2))
> plot(fit, newdata = newdata, showName = TRUE)
Error in get(method[[1]]) : object 'last.bumpup' not found
Calls: <Anonymous> ... drawDetails -> drawDetails.dlgrob -> apply.method -> get
Execution halted
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'gaussian_process_cv':
  'ncomp'

Documented arguments not in \usage in documentation object 'get_samples_from_strata':
  'starta'

Documented arguments not in \usage in documentation object 'ith_subsets_ortho_diss':
  'remove'

Documented arguments not in \usage in documentation object 'pca_nipals':
  'Y'

Documented arguments not in \usage in documentation object 'predict_gaussian_process':
  'b'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> nameEx("summary.reslr_output")
> ### * summary.reslr_output
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: summary.reslr_output
> ### Title: Produces summaries and convergence diagnostics for an object
> ###   created with 'reslr_mcmc'.
> ### Aliases: summary.reslr_output
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.36 0.05 1.41 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Documented arguments not in \usage in documentation object 'time_roll':
  'df'

Documented arguments not in \usage in documentation object 'validate_auto_rate':
  'df'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
Documented arguments not in \usage in documentation object 'get.V':
  'ct.lst'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs      1.6Mb
    models    1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
Rd files without \alias:
  'retry-package.Rd'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Running examples in 'RevGadgets-Ex.R' failed
The error most likely occurred in:

> ### Name: rerootPhylo
> ### Title: Reroot Phylo
> ### Aliases: rerootPhylo
> 
> ### ** Examples
> 
> 
> file <- system.file("extdata",
+                     "sub_models/primates_cytb_GTR_MAP.tre",
+                     package="RevGadgets")
> tree <- readTrees(paths = file)

  |                                              
  |                                        |   0%
  |                                              
  |========================================| 100%
> # root with one taxon
> tree_rooted <- rerootPhylo(tree = tree, outgroup = "Galeopterus_variegatus")
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Documented arguments not in \usage in documentation object 'compareChecksum.GenericDataFile':
  'verbose'

Documented arguments not in \usage in documentation object 'dim.GenericTabularFile':
  '...'

Documented arguments not in \usage in documentation object 'dsApplyInPairs.GenericDataFileSet':
  'ds'

Documented arguments not in \usage in documentation object 'GenericDataFile$fromFile':
  'unknown'

Documented arguments not in \usage in documentation object 'gzip.GenericDataFile':
  'verbose'

Documented arguments not in \usage in documentation object 'readChecksum.ChecksumFile':
  'verbose'

Documented arguments not in \usage in documentation object 'writeChecksum.GenericDataFile':
  'verbose'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'obs2Optim':
  'BIC'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
installed size is 100.0Mb
  sub-directories of 1Mb or more:
    doc        3.3Mb
    gdal       2.9Mb
    libs      81.6Mb
    pictures   1.3Mb
    proj       8.3Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Using_Rgff.Rmd' using rmarkdown

Quitting from lines 344-349 [unnamed-chunk-23] (Using_Rgff.Rmd)
Error: processing vignette 'Using_Rgff.Rmd' failed with diagnostics:
Package "rtracklayer" is required to convert from GTF to GFF3. Please install it.
--- failed re-building 'Using_Rgff.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs    2.6Mb
Documented arguments not in \usage in documentation object 'rgl.fns':
  'tag' 'tags'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) columbus.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) columbus.Rd:30: Escaped LaTeX specials: \$
Argument items with no description in Rd object 'MapBackground':
  'lat' 'lon'
Argument items with no description in Rd object 'plotOSM':
  'add' 'removeMargin'
Argument items with no description in Rd object 'plotOSMtile':
  'add' 'raster'
Argument items with no description in Rd object 'qbbox':
  'TYPE' 'verbose'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown

Quitting from lines 40-46 [unnamed-chunk-1] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
package or namespace load failed for 'phytools':
 object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'dimnames.AbstractFileArray':
  '...'

Documented arguments not in \usage in documentation object 'length.AbstractFileArray':
  '...'

Documented arguments not in \usage in documentation object 'readContiguousValues.AbstractFileArray':
  'length'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    lib    3.3Mb
    libs   4.1Mb
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object 'rioja-internal':
  '.rmse'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'inner_t_index_calculation':
  'param_'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/rivnet.Rcheck/00install.out' for details.
Found the following possibly unsafe calls:
File 'rJava/R/import.R':
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File 'rJava/R/jinit.R':
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.4/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    include   2.9Mb
    libs      2.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    extdata  23.8Mb
Invalid package aliases in Rd file 'rkt-package.Rd':
  'tkt-package'
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
Documented arguments not in \usage in documentation object 'ns_env':
  'env'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
GNU make is a SystemRequirements.
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    hdf5     16.0Mb
    include   6.5Mb
    lib       2.6Mb
    libs      8.2Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'fitted.values.margint':
  'fitted.values.margint'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
--- re-building 'CI_fix.Rmd' using rmarkdown
--- finished re-building 'CI_fix.Rmd'

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

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

Quitting from lines 20-83 [setup] (New_rmcorr_paper_analyses_figures.Rmd)
Error: processing vignette 'New_rmcorr_paper_analyses_figures.Rmd' failed with diagnostics:
package 'arm' could not be loaded
--- failed re-building 'New_rmcorr_paper_analyses_figures.Rmd'

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/rmfanova.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/rmgarch.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs       1.0Mb
    minizinc   2.3Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'bind':
  '.single_on_bind'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'WeightsFun_1C_1AIR':
  'x'

Documented arguments not in \usage in documentation object 'assert_col_vec_3C':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'ols':
  'penalty'
Argument items with no description in Rd object 'rmsMisc':
  'fit1'
Argument items with no description in Rd object 'val.surv':
  'xlim'
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:
  common_stub.c:74:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/rmumps.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
GNU make is a SystemRequirements.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(Matrix)
  > library(methods)
  > library(Rcpp)
  > if (getRversion() >= "3.4.0") {
  +   library(slam)
  + }
  > library(rmumps)
  > test_check("rmumps")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_rmumps.R:23:1'): (code run outside of `test_that()`) ───────────
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
Running examples in 'rmweather-Ex.R' failed
The error most likely occurred in:

> ### Name: rmw_predict
> ### Title: Function to predict using a *ranger* random forest.
> ### Aliases: rmw_predict
> 
> ### ** Examples
> 
> 
> # Load package
> 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

> 
> # Prepare example data
> data_london_prepared <- data_london %>% 
+   filter(variable == "no2") %>% 
+   rmw_prepare_data()
> 
> # Make a prediction with the examples
> vector_prediction <- rmw_predict(
+   model_london, 
+   df = data_london_prepared
+ )
> 
> 
> # Make a prediction with standard errors too
> list_prediction <- rmw_predict(
+   model_london, 
+   df = data_london_prepared,
+   se = TRUE
+ )
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(rmweather)
  > 
  > test_check("rmweather")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 38 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_02_rmw_functions.R:169:3'): Test normalising function with standard error calculation ──
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─testthat::expect_identical(...) at test_02_rmw_functions.R:169:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─rmweather::rmw_predict(model, df, se = TRUE, n_cores = 1)
   5.   ├─stats::predict(...)
   6.   └─ranger:::predict.ranger(...)
   7.     ├─stats::predict(...)
   8.     └─ranger:::predict.ranger.forest(...)
   9.       └─ranger:::rInfJack(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 38 ]
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RNAseqQC.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rnaturalearthhires'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.3Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'SanitizeURL':
  'bad.str'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> flush(stderr()); flush(stdout())
> 
> ### Name: npn_stations_with_spp
> ### Title: Get Stations with Species
> ### Aliases: npn_stations_with_spp
> 
> ### ** Examples
> 
> ## Not run: 
> ##D npn_stations_with_spp(speciesid = c(52,53,54))
> ##D npn_stations_with_spp(speciesid = 53)
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  0.78 0.03 0.81 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.7Mb
Documented arguments not in \usage in documentation object 'internals_for_RobAStBase_plot':
  'panelFirst'

Documented arguments not in \usage in documentation object 'internals_for_RobAStBase':
  'L2fam'
Objects in \usage without \alias in documentation object 'internals_for_RobAStBase':
  '.evalListRec' '.filterEargsWEargList'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
Invalid package aliases in Rd file '0RobRDA-package.Rd':
  'RobRDA-package'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'internal_interpolate_helpers_for_RobExtremes':
  'upRad.s'
Objects in \usage without \alias in documentation object 'internal_interpolate_helpers_for_RobExtremes':
  '.getPsi.wL' '.getPsi.P'

Objects in \usage without \alias in documentation object 'rescaleFunction-methods':
  'rescaleFunction'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'createITPSplineResult':
  'measure'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
checkRd: (7) NEWS.Rd:320: Tag \bold is invalid in a \code block
Argument items with no description in Rd object 'nlrob.control':
  '\dots'
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\emmintrin.h:131:24: warning: array subscript '__m128d_u[0]' is partly outside array bounds of 'Eigen::internal::plain_matrix_type<Eigen::Product<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>, Eigen::Transpose<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false> >, 0>, Eigen::Dense>::type [1]' {aka 'Eigen::Matrix<double, 1, 1, 0, 1, 1> [1]'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.4/RobustGaSP.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
Documented arguments not in \usage in documentation object 'Sample':
  'interval_data'

Objects in \usage without \alias in documentation object 'neg_log_marginal_post_approx_ref_ppgasp':
  'neg_log_marginal_post_approx_ref'

Objects in \usage without \alias in documentation object 'separable_multi_kernel':
  'separable_kernel'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              1.3Mb
    simulationStudy   1.6Mb
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'choose.test':
  'Xpaired' 'Ypaired' 'Xextra' 'Yextra' 'mc.rep'
Argument items with no description in Rd object 'multinom.test':
  'X' 'Y' 'alternative' 'correct' 'perm' 'mc.rep' 'method' 'verbose'
  'mode' 'useC'
Argument items with no description in Rd object 'mw.mw.2.perm':
  'X' 'Y' 'Xprime' 'Yprime' '.corr' 'mc.rep' 'alternative' 'verbose'
Argument items with no description in Rd object 'pm.wilcox.test':
  'Xpaired' 'Ypaired' 'Xextra' 'Yextra' 'alternative' 'verbose'
Argument items with no description in Rd object 'sim.partially.matched':
  'meanRatio' 'sdRatio' 'within.sd' 'type' 'hyp'
Argument items with no description in Rd object 'wmw.paired.replicates.test':
  'X' 'Y' 'alternative' 'correct' 'perm' 'mc.rep' 'method' 'verbose'
  'mode' 'useC'
Problems with news in 'NEWS.md':
No news entries found.
Objects in \usage without \alias in documentation object 'gettptnfpfn-defunct':
  'gettptnfpfn'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Rogue.Rcheck/00install.out' for details.
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'add_matches_columns':
  'Matches'

Documented arguments not in \usage in documentation object 'run_checks_two':
  'lookback' 'standard_deviaion' 'match_on' 'model_type'

Documented arguments not in \usage in documentation object 'trim_pool':
  'standard_deviaion'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
Auto-generated content requiring editing in Rd object 'roloc-package':
  \references: '~~ Literature or other references for background information ~~'
  \seealso: '~~ Optional links to other man pages, e.g. ~~'
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
Documented arguments not in \usage in documentation object 'DOLLAR.Class':
  '...'

Documented arguments not in \usage in documentation object 'DOLLAR< -.Class':
  '...'

Documented arguments not in \usage in documentation object 'getMethods.Class':
  'unqiue'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'internal_interpolate_helpers':
  'upRad.s' 'withSmooth'
Assignments in \usage in documentation object 'internal_interpolate_helpers':
  .readGridFromCSV <- function(fromFileCSV) .generateInterpGrid(thGrid, 
      PFam, toFileCSV = "temp.csv", getFun = .getLMGrid, ..., modifyfct, 
      nameInSysdata, GridFileName, withPrint = TRUE, len = 13)

Objects in \usage without \alias in documentation object 'internals_for_ROptEst_robest':
  '.constructArg.list' '.fix.in.defaults' '.pretreat' '.check.eps'
  '.isOKsteps' '.isOKfsCor'

Documented arguments not in \usage in documentation object 'internals_for_ROptEst_Cniperplots':
  'origCl'

Objects in \usage without \alias in documentation object 'internals_for_ROptEst':
  '.isVirginW'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ROracle.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   1.5Mb
Invalid package aliases in Rd file 'A.Introduction-RoughSets.Rd':
  'A.Introduction-RoughSets-package'
Invalid package aliases in Rd file 'B.Introduction-FuzzyRoughSets.Rd':
  'B.Introduction-FuzzyRoughSets-package'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RPANDA.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'RandomFields'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/rPanglaoDB.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object 'rpart-internal':
  'rpart.anova' 'rpart.class' 'rpart.poisson' 'rpartco'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Rphylopars.Rcheck/00install.out' for details.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Title: Save a PhyloPic image
> ### Aliases: save_phylopic
> 
> ### ** Examples
> 
> ## Not run: 
> ##D # Get image data
> ##D img <- get_phylopic("27356f15-3cf8-47e8-ab41-71c6260b2724")
> ##D # Save file
> ##D save_phylopic(img = img, path = "./phylopic.png",
> ##D               width = 500, height = 500)
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  5.25 0.28 27.94 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'pgCheckGeom':
  'namechar'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  vendor/boost/intrusive/detail/slist_node.hpp:56:16: warning: pointer used after 'void operator delete(void*, std::size_t)' [-Wuse-after-free]
  vendor/boost/intrusive/detail/hook_traits.hpp:77:10: warning: pointer used after 'void operator delete(void*, std::size_t)' [-Wuse-after-free]
See 'd:/Rcompile/CRANpkg/local/4.4/RPostgres.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'rrcov-utils':
  'tol' 'sv' 'n' 'p'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'RNAPlot':
  'seqTF'
Argument items with no description in Rd object 'aptPlotCT':
  'seqTF'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RRphylo.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/rr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object '[.RspDocument':
  '...'

Documented arguments not in \usage in documentation object 'RspEvalDirective':
  'attributes'

Documented arguments not in \usage in documentation object 'RspExpression':
  'object'

Documented arguments not in \usage in documentation object 'RspIncludeDirective':
  'attributes'

Documented arguments not in \usage in documentation object 'buildNonSweaveVignette':
  'pathname'

Documented arguments not in \usage in documentation object 'buildNonSweaveVignettes':
  'path' 'pattern'

Documented arguments not in \usage in documentation object 'exprToCode.RspSourceCodeFactory':
  'expr'

Documented arguments not in \usage in documentation object 'getContent.RspText':
  'unescaped'

Documented arguments not in \usage in documentation object 'toSourceCode.RspSourceCodeFactory':
  'expr'

Documented arguments not in \usage in documentation object 'trim.RspDocument':
  'envir'

Documented arguments not in \usage in documentation object 'writeResponse.RspResponse':
  'collapse' 'sep'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'rrum_helper':
  'deltas'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'create_tool':
  'character'

Documented arguments not in \usage in documentation object 'update_parameters_file':
  'param'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  websockets.c:21:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  standalone.c:160:301: warning: format '%ld' expects argument of type 'long int', but argument 16 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:3788:97: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4133:62: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4435:118: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4804:106: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4824:147: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4836:114: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4864:121: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4870:139: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  qap_encode.c:142:17: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'rlen_t' {aka 'long long int'} [-Wformat=]
  websockets.c:513:119: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/Rserve.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
GNU make is a SystemRequirements.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.4/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'ApiRequest':
  'report.description'

Documented arguments not in \usage in documentation object 'BuildLineItemSegment':
  'elements'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.4Mb
    help   1.4Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RSP.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.8Mb
    libs   9.5Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib    2.1Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'SetHash':
  '\dots'
Invalid package aliases in Rd file 'Rstpm2-package.Rd':
  'Rstpm2-package'
Documented arguments not in \usage in documentation object 'calculate.var.np':
  'sone' 'szero' 'yone' 'yzero'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/rsvd.Rcheck/00install.out' for details.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is 40.0Mb
  sub-directories of 1Mb or more:
    libs    1.1Mb
    swipl  38.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R           1.4Mb
    bootstrap   1.6Mb
    doc         1.4Mb
    help        2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Rtapas.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    rmarkdown   9.4Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Undocumented code objects:
  'crossprod' 'tcrossprod'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'summary.trimbatch':
  'x'

Documented arguments not in \usage in documentation object 'trim_workhorse':
  'max_beta'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
Documented arguments not in \usage in documentation object 'TWIT_paginate_max_id':
  'parse'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'tidy_pi_traces':
  'mix_indiv_tib'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
Running examples in 'ruimtehol-Ex.R' failed
The error most likely occurred in:

> ### Name: embed_docspace
> ### Title: Build a Starspace model for content-based recommendation
> ### Aliases: embed_docspace
> 
> ### ** Examples
> 
> library(udpipe)
Error: package or namespace load failed for 'udpipe':
 object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'MEM_MIDAS_lr_pred_no_skew':
  'daily_ret'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object 'printHTML.trackInfo':
  'printHTML.trackInfo'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object '.is_datetime_valid':
  '(`character`)'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'hsize':
  'sizes' 'digits' 'units' 'bytes'

Documented arguments not in \usage in documentation object 'timestamp.Verbose':
  'stamp'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: 'glmmADMB'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs      5.2Mb
Problems with news in 'NEWS.md':
No news entries found.
Documented arguments not in \usage in documentation object 'summary.rv':
  'all.levels'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'matmult':
  '%*%.rv'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rWCVPdata'
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/rwicc.Rcheck/00install.out' for details.
Documented arguments not in \usage in documentation object 'wind.fit_int':
  'X'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mapBubbles.Rd:62: Escaped LaTeX specials: \$
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/rwty.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
Documented arguments not in \usage in documentation object 'rxErrTypeCombine':
  'newTransform'

Documented arguments not in \usage in documentation object 'rxRepR0_':
  'number'

Documented arguments not in \usage in documentation object 'rxSetupScale':
  'inits'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'unix'
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object '.LoadDataFile':
  'remapcells'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'predict.s2netR':
  '...'
Argument items with no description in Rd object 'print.s2Data':
  '\dots'
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
matrixOps:
  function(x, y)
matrixOps.S7_object:
  function(e1, e2)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'file_status':
  'A'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
[1] "id_col"


[[2]]
[[2]][[1]]
[1] "measure_col"

[[2]][[2]]
[1] "label"


> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.33 0.61 3.93 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object 'SAMM-package':
  \seealso: '~~ Optional links to other man pages, e.g. ~~'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  13.4Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   1.3Mb
Package suggested but not available for checking: 'networkTomography'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'santoku-cast':
  'santoku_cast_common.default' 'santoku_cast_common.double'
  'santoku_cast_common.Date' 'santoku_cast_common.POSIXct'
  'santoku_cast_common.ts' 'santoku_cast_common.zoo'
  'santoku_cast_common.integer64' 'santoku_cast_common.hexmode'
  'santoku_cast_common.octmode'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'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: 'FitARMA'
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
Argument items with no description in Rd object 'creer_graphe':
  'groupes'
Argument items with no description in Rd object 'fichiers':
  'groupes'
'library' or 'require' call to 'progress' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'item_rm_recursive':
  'sb_id'

Documented arguments not in \usage in documentation object 'session_age':
  'sb_id' '...'

Documented arguments not in \usage in documentation object 'session_expired':
  'sb_id' '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/scAnnotate.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/scCustomize.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/scDiffCom.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'DuoClustering2018'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/scGate.Rcheck/00install.out' for details.
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/scistreer.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/scMappR.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Failed with error:  'package 'SummarizedExperiment' could not be loaded'
  Error loading dataset 'sce':
   Error in .requirePackage(package) : 
    unable to find required package 'SingleCellExperiment'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
Running examples in 'SC.MEB-Ex.R' failed
The error most likely occurred in:

> ### Name: find_neighbors2
> ### Title: find_neighbors2.
> ### Aliases: find_neighbors2
> 
> ### ** Examples
> 
> data(sce)
> platform = "ST"
> Adj <- find_neighbors2(sce, platform)
Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
Execution halted
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/scoper.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'plot':
  'plot.discretization'

S3 methods shown with full name in documentation object 'predict':
  'predict.discretization' 'predict.reject_infered'

S3 methods shown with full name in documentation object 'summary':
  'summary.discretization'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'anndata.Rmd' using rmarkdown
--- finished re-building 'anndata.Rmd'

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

--- re-building 'simulated-data.Rmd' using rmarkdown
--- finished re-building 'simulated-data.Rmd'

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

Quitting from lines 26-40 [load_data] (singlecellexperiment.Rmd)
Error: processing vignette 'singlecellexperiment.Rmd' failed with diagnostics:
package 'SummarizedExperiment' could not be loaded
--- failed re-building 'singlecellexperiment.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/scperturbR.Rcheck/00install.out' for details.
Running examples in 'scpoisson-Ex.R' failed
The error most likely occurred in:

> ### Name: LouvainDepart
> ### Title: Louvain clustering using departure as data representation
> ### Aliases: LouvainDepart
> 
> ### ** Examples
> 
> 
> set.seed(1234)
> test_set <- matrix(rpois(500, 2), nrow = 20)
> rownames(test_set) <- paste0("gene", 1:nrow(test_set))
> colnames(test_set) <- paste0("cell", 1:ncol(test_set))
> LouvainDepart(test_set)
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'scpoissonmodel.Rmd' using rmarkdown

Quitting from lines 79-85 [example3] (scpoissonmodel.Rmd)
Error: processing vignette 'scpoissonmodel.Rmd' failed with diagnostics:
object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'scpoissonmodel.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SCRIP.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/scRNAstat.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Failed with error:  'package 'SummarizedExperiment' could not be loaded'
  Error loading dataset 'test_sce_data':
   Error in .requirePackage(package) : 
    unable to find required package 'SingleCellExperiment'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/sdcTable.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'INLA'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Package unavailable to check Rd xrefs: 'INLA'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'parse_search_analytics':
  'pn'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
Documented arguments not in \usage in documentation object '%>%':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   2.0Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'Using_secsse.Rmd' using rmarkdown

Quitting from lines 50-59 [unnamed-chunk-5] (Using_secsse.Rmd)
Error: processing vignette 'Using_secsse.Rmd' failed with diagnostics:
package 'phytools' could not be loaded
--- failed re-building 'Using_secsse.Rmd'

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'SeedMatchR.Rmd' using rmarkdown

Quitting from lines 47-51 [unnamed-chunk-3] (SeedMatchR.Rmd)
Error: processing vignette 'SeedMatchR.Rmd' failed with diagnostics:
package or namespace load failed for 'GenomicFeatures':
 objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
--- failed re-building 'SeedMatchR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'spgrass6'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SEIRfansy.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Running examples in 'SelectionBias-Ex.R' failed
The error most likely occurred in:

> ### Name: SVboundparametersM
> ### Title: Sensitivity parameters for the Smith and VanderWeele bound
> ### Aliases: SVboundparametersM
> 
> ### ** Examples
> 
> 
> # Example with no selection bias.
> V = matrix(c(1, 0, 0.1, 0.9), ncol = 2)
> U = matrix(c(1, 0, 0.1, 0.9), ncol = 2)
> Tr = c(0, 1)
> Y = c(0, 0, 1)
> S = matrix(c(1, 0, 0, 0, 1, 0, 0, 0), nrow = 2, byrow = TRUE)
> probT1 = 0.534
> probT0 = 0.534
> SVboundparametersM(whichEst = "RR_tot", Vval = V, Uval = U, Tcoef = Tr,
+   Ycoef = Y, Scoef = S, Mmodel = "P", pY1_T1_S1 = probT1, pY1_T0_S1 = probT0)
     [,1]                [,2]  
[1,] "BF_1"              1     
[2,] "BF_0"              1     
[3,] "RR_UY|T=1"         1.6827
[4,] "RR_UY|T=0"         1.6827
[5,] "RR_SU|T=1"         1     
[6,] "RR_SU|T=0"         1     
[7,] "Reverse treatment" FALSE 
> 
> # Example with selection bias. DGP from the zika example.
> V = matrix(c(1, 0, 0.85, 0.15), ncol = 2)
> U = matrix(c(1, 0, 0.5, 0.5), ncol = 2)
> Tr = c(-6.2, 1.75)
> Y = c(-5.2, 5.0, -1.0)
> S = matrix(c(1.2, 2.2, 0.0, 0.5, 2.0, -2.75, -4.0, 0.0), ncol = 4)
> probT1 = 0.286
> probT0 = 0.004
> SVboundparametersM(whichEst = "RR_sub", Vval = V, Uval = U, Tcoef = Tr,
+   Ycoef = Y, Scoef = S, Mmodel = "L", pY1_T1_S1 = probT1, pY1_T0_S1 = probT0)
Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SelectionBias.Rmd' using rmarkdown

Quitting from lines 145-156 [unnamed-chunk-4] (SelectionBias.Rmd)
Error: processing vignette 'SelectionBias.Rmd' failed with diagnostics:
objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
--- failed re-building 'SelectionBias.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'min.abs':
  'min.abs'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/semPlot.Rcheck/00install.out' for details.
Running examples in 'semptools-Ex.R' failed
The error most likely occurred in:

> ### Name: change_node_label
> ### Title: Change node labels
> ### Aliases: change_node_label
> 
> ### ** Examples
> 
> library(semPlot)
Error: package or namespace load failed for 'semPlot':
 objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/sem.Rcheck/00install.out' for details.
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/sensiPhy.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fahst.rd:39: Escaped LaTeX specials: \^
checkRd: (-1) fahst.rd:36: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:46: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:42: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:43: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:49: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:44: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:46: Escaped LaTeX specials: \^
checkRd: (-1) hsortplot.rd:24: Escaped LaTeX specials: \^
checkRd: (-1) nappesortplot.Rd:30: Escaped LaTeX specials: \^
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checkRd: (-1) plot.fahst.rd:45: Escaped LaTeX specials: \^
checkRd: (-1) plot.fasnt.Rd:47: Escaped LaTeX specials: \^
checkRd: (-1) plot.fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) print.fahst.rd:22: Escaped LaTeX specials: \^
checkRd: (-1) print.fasnt.Rd:22: Escaped LaTeX specials: \^
checkRd: (-1) print.fast.Rd:22: Escaped LaTeX specials: \^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running 'testthat.R' [108s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > library("testthat")
  > library("sentopics")
  > 
  > if (Sys.getenv("R_COVR") != "true") {
  +   test_check("sentopics")
  + } else {
  +   test_check("sentopics", reporter = default_reporter())
  +   # test_check("sentopics", reporter = LocationReporter)
  + }
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 321 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-parallel_chains.R:97:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-conversions.R:12:3'): from STM ─────────────────────────────────
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─stm::stm(...) at test-conversions.R:12:2
   2.   └─stm:::stm.control(documents, vocab, settings, model)
   3.     └─stm:::stm.init(documents, settings)
   4.       └─stm:::gram(mat)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 321 ]
  Error: Test failures
  Execution halted
Auto-generated content requiring editing in Rd object 'seqCBS-package':
  \details: '...the package, including the most important ~~ ~~ functions ~~'
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SeqFeatR.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'different_thinners.Rmd' using rmarkdown
--- finished re-building 'different_thinners.Rmd'

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

Quitting from lines 83-85 [unnamed-chunk-14] (simulate_rnaseq.Rmd)
Error: processing vignette 'simulate_rnaseq.Rmd' failed with diagnostics:
package 'SummarizedExperiment' could not be loaded
--- failed re-building 'simulate_rnaseq.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
Argument items with no description in Rd object 'sequential.design':
  '\dots'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/serrsBayes.Rcheck/00install.out' for details.
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Seurat.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'jc_clc_perm_impl':
  'a'

Documented arguments not in \usage in documentation object 'local_g_spt':
  'n_sim'

Documented arguments not in \usage in documentation object 'permute_listw':
  'a'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown

Quitting from lines 44-48 [unnamed-chunk-3] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `loadNamespace()`:
! there is no package called 'prettymapr'
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 100.5Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    gdal     2.9Mb
    libs    83.1Mb
    proj     8.3Mb
    sqlite   1.5Mb
Found export directive that requires package 'methods':
  'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'package_sgmodel.Rd':
  'package_sgmodel-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
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    data   6.7Mb
checkRd: (-1) gPLS.Rd:72: Escaped LaTeX specials: \^
checkRd: (-1) gPLS.Rd:74: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:67: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:69: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:75: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:77: Escaped LaTeX specials: \^
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.0Mb
Missing or unexported object: 'Matrix::crossprod'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rCOSA'
Package unavailable to check Rd xrefs: 'rCOSA'
Package suggested but not available for checking: 'hydromad'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/shazam.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'shiny_models':
  'original_data'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    www   8.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'shipunov-Ex.R' failed
The error most likely occurred in:

> ### Name: MrBayes
> ### Title: Calls MrBayes
> ### Aliases: MrBayes
> ### Keywords: interface
> 
> ### ** Examples
> 
> require(ips)
Loading required package: ips
Loading required package: ape
Error: package or namespace load failed for 'ips':
 object 'crossprod' is not exported by 'namespace:Matrix'
> data(ips.cox1)
Warning in data(ips.cox1) : data set 'ips.cox1' not found
> x <- ips.cox1[, 100:140]
Error: object 'ips.cox1' not found
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    help      1.7Mb
    libs      1.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Signac.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SIGN.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'estThetaRow':
  'theta'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'print_info':
  'line'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in 'simITS-Ex.R' failed
The error most likely occurred in:

> ### Name: aggregate_simulation_results
> ### Title: Test a passed test statistic on the simulated data
> ### Aliases: aggregate_simulation_results
> 
> ### ** Examples
> 
> predictions = process_outcome_model( "pbail", mecklenberg,
+                                     t0=0, R = 5,
+                                     summarize = FALSE, smooth=FALSE )
Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'simple_ITS_example.Rmd' using rmarkdown

Quitting from lines 64-69 [unnamed-chunk-4] (simple_ITS_example.Rmd)
Error: processing vignette 'simple_ITS_example.Rmd' failed with diagnostics:
objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
--- failed re-building 'simple_ITS_example.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object 'make_kernel_dist':
  'Umax'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'interval_labels':
  'format'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'SimplifyStats-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SimRAD.Rcheck/00install.out' for details.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'fg_step_tab_pp'
Invalid package aliases in Rd file 'SimReg-package.Rd':
  'SimReg3-package'
Documented arguments not in \usage in documentation object 'sim_founderRVstatus':
  'intro_RV'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++14: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SIPmg.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   1.5Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'management.prob':
  '...'
Argument items with no description in Rd object 'mng.tree.removal':
  '\dots'
Argument items with no description in Rd object 'prep.common.vars.fun':
  '\dots'
Argument items with no description in Rd object 'recr.BBG2008':
  'common.vars'
Running examples in 'sketching-Ex.R' failed
The error most likely occurred in:

> ### Name: sketch
> ### Title: Sketch
> ### Aliases: sketch
> 
> ### ** Examples
> 
> ## Least squares: sketch and solve
> # setup
> n <- 1e+6 # full sample size
> d <- 5    # dimension of covariates
> m <- 1e+3 # sketch size
> # generate psuedo-data
> X <- matrix(stats::rnorm(n*d), nrow = n, ncol = d)
> beta <- matrix(rep(1,d), nrow = d, ncol = 1)
> eps <- matrix(stats::rnorm(n), nrow = n, ncol = 1)
> Y <- X %*% beta + eps
> intercept <- matrix(rep(1,n), nrow = n, ncol = 1)
> # full sample including the intercept term
> fullsample <- cbind(Y,intercept,X)
> # generate a sketch using CountSketch
> s_cs <-  sketch(fullsample, m, "countsketch")
> # solve without the intercept
> ls_cs <- lm(s_cs[,1] ~ s_cs[,2] - 1)
> # generate a sketch using SRHT
> s_srht <-  sketch(fullsample, m, "srht")
Error: object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sketching)
  > 
  > test_check("sketching")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 7 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_AK.R:37:3'): Different methods generate different results II ───
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─sketching::sketch(fullsample, m, method = "srht") at test_AK.R:37:2
   2. │ └─base::cbind(data_srht, phangorn::fhm(data_j))
   3. └─base::loadNamespace(x)
   4.   └─base::namespaceImportFrom(...)
   5.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 7 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'sketching_vignette.Rmd' using rmarkdown

Quitting from lines 275-290 [unnamed-chunk-8] (sketching_vignette.Rmd)
Error: processing vignette 'sketching_vignette.Rmd' failed with diagnostics:
object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'sketching_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in documentation object 'to_shiny_tag':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'kmndirs'
Missing or unexported objects:
  'Matrix::crossprod' 'Matrix::tcrossprod'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object 'calculate_gefficiency':
  'RunMatrix'

Documented arguments not in \usage in documentation object 'constructRunMatrix':
  'Levelvector'

Documented arguments not in \usage in documentation object 'effectpower':
  'X'

Documented arguments not in \usage in documentation object 'gen_momentsmatrix':
  'Levelvector'

Documented arguments not in \usage in documentation object 'generate_noise_block':
  'RunMatrix'

Documented arguments not in \usage in documentation object 'genhypmatrix':
  'Parameters' 'Levels' 'G'

Documented arguments not in \usage in documentation object 'genparammatrix':
  'Parameters' 'Levels' 'G'

Documented arguments not in \usage in documentation object 'priorlevels':
  'Levelvector'

Documented arguments not in \usage in documentation object 'reduceRunMatrix':
  'ModelMatrix'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Error(s) in re-building vignettes:
--- re-building 'skyscapeR.Rmd' using rmarkdown

Quitting from lines 197-199 [unnamed-chunk-16] (skyscapeR.Rmd)
Error: processing vignette 'skyscapeR.Rmd' failed with diagnostics:
Timeout was reached: [www.heywhatsthat.com] Connection timeout after 10013 ms
--- failed re-building 'skyscapeR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'capacity_logreg_testing':
  'maxNWts'

Documented arguments not in \usage in documentation object 'mi_logreg_testing':
  'maxNWts'

Documented arguments not in \usage in documentation object 'output_graphs_main':
  'path'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SmallCountRounding.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'gurobi'
Auto-generated content requiring editing in Rd object 'smallstuff-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Unknown package 'InformationValue' in Rd xrefs
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SMDIC.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
Documented arguments not in \usage in documentation object 'aux_cs':
  'dists'

Documented arguments not in \usage in documentation object 'aux_gauss':
  'dists'

Documented arguments not in \usage in documentation object 'aux_gw':
  'dists'

Documented arguments not in \usage in documentation object 'aux_mat':
  'mat_list1' 'mat_list2' 'x' 'y' 'return_single'

Documented arguments not in \usage in documentation object 'aux_matern':
  'dists'

Documented arguments not in \usage in documentation object 'aux_pexp':
  'dists'

Documented arguments not in \usage in documentation object 'aux_spher':
  'dists'

Documented arguments not in \usage in documentation object 'aux_tapmat':
  'dists'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'SMLE-package.Rd':
  'smle-package'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'smoke-package':
  \details: '...the package, including the most important ~~ ~~ functions ~~'
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'doMC'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.3Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'lseq'
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object 'smotefamily-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
Objects in \usage without \alias in documentation object 'sm-internal':
  'sm.check.data'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> nameEx("snvec")
> ### * snvec
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: snvec
> ### Title: Calculate Earth’s Obliquity and Precession in the Past
> ### Aliases: snvec
> 
> ### ** Examples
> 
> # default call
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  0.95 0.17 1.12 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     3.3Mb
    doc   1.1Mb
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.solveEnv'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.3Mb
    libs   1.7Mb
Documented arguments not in \usage in documentation object 'som.nn.do.train':
  'model'

Documented arguments not in \usage in documentation object 'som.nn.som.internal':
  'rlen'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'plot.predictions':
  'plot.predictions'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'path2name':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'averageMatrices':
  'aggFun'

Documented arguments not in \usage in documentation object '.detectNLP':
  'orig_x'

Documented arguments not in \usage in documentation object 'getSmoothSpectrum':
  'a'

Documented arguments not in \usage in documentation object 'htmlPlots':
  'myfolder' 'myfiles'

Documented arguments not in \usage in documentation object 'interpolate':
  'manualUnvoiced'

Documented arguments not in \usage in documentation object 'parabPeakInterpol':
  'points'

Documented arguments not in \usage in documentation object 'processAudio':
  'summaryFun'

Documented arguments not in \usage in documentation object 'pseudoLog':
  'approximate'

Documented arguments not in \usage in documentation object 'pseudoLog_undo':
  'approximate'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SoupX.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'r2cytoscape'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NLMR'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R   4.6Mb
Documented arguments not in \usage in documentation object '.findModuleName':
  'modules'

Documented arguments not in \usage in documentation object '.runCodeChecks':
  'message'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'NLMR'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/spaMM.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    java   3.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SparseBiplots.Rcheck/00install.out' for details.
Unknown package 'sparsebn' in Rd xrefs
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/sparseFLMM.Rcheck/00install.out' for details.
Missing or unexported object: 'Matrix::crossprod'
Running 'testthat.R' [137s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sparsegl)
  > 
  > test_check("sparsegl")
  Loading required package: Matrix
  Loaded glmnet 4.1-8
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 150 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • skipping all macro irwls tests. (1): 'test-sgl_irwls.R:112:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-risk_estimation.R:33:3'): check if function exact_df() works as expected ──
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(length(exact_df(out, X)), 100) at test-risk_estimation.R:33:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─sparsegl:::exact_df(out, X)
  ── Error ('test-risk_estimation.R:66:3'): risk estimation functions reasonably ──
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─testthat::expect_named(...) at test-risk_estimation.R:66:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─sparsegl::estimate_risk(out_sparse, X)
   5. └─sparsegl:::estimate_risk.lsspgl(out_sparse, X)
   6.   └─sparsegl:::exact_df(object, x)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 150 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'sparsegl.Rmd' using rmarkdown

Quitting from lines 260-261 [unnamed-chunk-10] (sparsegl.Rmd)
Error: processing vignette 'sparsegl.Rmd' failed with diagnostics:
'crossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'sparsegl.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Missing or unexported object: 'Matrix::crossprod'
Running examples in 'sparseHessianFD-Ex.R' failed
The error most likely occurred in:

> ### Name: sparseHessianFD
> ### Title: sparseHessianFD
> ### Aliases: sparseHessianFD
> 
> ### ** Examples
> 
> ## Log posterior density of hierarchical binary choice model. See vignette.
> set.seed(123)
> data("binary_small")
> N <- length(binary[["Y"]])
> k <- NROW(binary[["X"]])
> T <- binary[["T"]]
> P <- rnorm((N+1)*k)
> priors <- list(inv.Sigma = rWishart(1,k+5,diag(k))[,,1],
+                inv.Omega = diag(k))
> true.hess <- binary.hess(P, binary, priors)
> pattern <- Matrix.to.Coord(Matrix::tril(true.hess))
> str(pattern)
List of 2
 $ rows: int [1:1310] 1 2 3 4 201 202 203 204 2 3 ...
 $ cols: int [1:1310] 1 1 1 1 1 1 1 1 2 2 ...
> obj <- sparseHessianFD(P, fn=binary.f, gr=binary.grad,
+        rows=pattern[["rows"]], cols=pattern[["cols"]],
+                       data=binary, priors=priors)
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sparseHessianFD)
  > 
  > test_check("sparseHessianFD")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 37 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_binary.R:53:5'): binary_example ────────────────────────────────
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─sparseHessianFD::sparseHessianFD(...) at test_binary.R:53:4
   2.   └─methods::new(`<chr>`, ...)
   3.     ├─methods::initialize(value, ...)
   4.     └─methods::initialize(value, ...)
   5.       └─.Object$initialize(...)
   6.         └─sparseHessianFD::coloring(L)
  ── Error ('test_complex.R:53:5'): binary_example_complex ───────────────────────
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─sparseHessianFD::sparseHessianFD(...) at test_complex.R:53:4
   2.   └─methods::new(`<chr>`, ...)
   3.     ├─methods::initialize(value, ...)
   4.     └─methods::initialize(value, ...)
   5.       └─.Object$initialize(...)
   6.         └─sparseHessianFD::coloring(L)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 37 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'sparseHessianFD.Rnw' using knitr

Quitting from lines 854-861 [usingSparseHessianFD1] (sparseHessianFD.Rnw)
Error: processing vignette 'sparseHessianFD.Rnw' failed with diagnostics:
'crossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'sparseHessianFD.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::crossprod'
'LazyData' is specified without a 'data' directory
Running examples in 'sparseLRMatrix-Ex.R' failed
The error most likely occurred in:

> ### Name: dim,sparseLRMatrix-method
> ### Title: Check the dimension of a sparseLRMatrix
> ### Aliases: dim,sparseLRMatrix-method
> 
> ### ** Examples
> 
> 
> set.seed(528491)
> 
> n <- 50
> m <- 40
> k <- 3
> 
> A <- rsparsematrix(n, m, 0.1)
> 
> U <- Matrix(rnorm(n * k), nrow = n, ncol = k)
> V <- Matrix(rnorm(m * k), nrow = m, ncol = k)
> 
> # construct the matrix, which represents A + U %*% t(V)
> X <- sparseLRMatrix(sparse = A, U = U, V = V)
> 
> dim(X)
[1] 50 40
> 
> s <- svds(X, 5)  # efficient
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sparseLRMatrix)
  Loading required package: Matrix
  > 
  > test_check("sparseLRMatrix")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-svds-matches.R:17:3'): singular values match ───────────────────
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─RSpectra::svds(X, 5) at test-svds-matches.R:17:2
   2. ├─sparseLRMatrix:::svds.sparseLRMatrix(X, 5)
   3. │ ├─RSpectra::svds(...)
   4. │ └─RSpectra:::svds.function(...)
   5. │   └─RSpectra:::svds_real_gen(...)
   6. └─sparseLRMatrix (local) `<fn>`(`<dbl>`, `<sprsLRMt[,40]>`)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::crossprod'
Running examples in 'sparseMVN-Ex.R' failed
The error most likely occurred in:

> ### Name: dmvn.sparse
> ### Title: Compute density from multivariate normal distribution
> ### Aliases: dmvn.sparse
> 
> ### ** Examples
> 
>    require(Matrix)
Loading required package: Matrix
>    m <- 20
>    p <- 2
>    k <- 4
> 
> ## build sample sparse covariance matrix
>    Q1 <- tril(kronecker(Matrix(seq(0.1,p,length=p*p),p,p),diag(m)))
>    Q2 <- cbind(Q1,Matrix(0,m*p,k))
>    Q3 <- rbind(Q2,cbind(Matrix(rnorm(k*m*p),k,m*p),Diagonal(k)))
>    V <- tcrossprod(Q3)
>    CH <- Cholesky(V)
> 
>    x <- rmvn.sparse(10,rep(0,p*m+k),CH, FALSE)
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sparseMVN)
  > 
  > test_check("sparseMVN")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_sparseMVN.R:19:5'): sparseMVN ──────────────────────────────────
  Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/sparsepca.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Documented arguments not in \usage in documentation object 'logit':
  'theta'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SpatialDDLS.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.1Mb
Argument items with no description in Rd object 'binarizer':
  '\dots'
Specified C++11: please drop specification unless essential
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat.data', 'spatstat',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'

Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package unavailable to check Rd xrefs: 'RandomFields'
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'
Package unavailable to check Rd xrefs: 'RandomFields'
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'spDataLarge'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
    etc   1.4Mb
Documented arguments not in \usage in documentation object 'hazard':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SPECK.Rcheck/00install.out' for details.
Documented arguments not in \usage in documentation object '%matches%':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Documented arguments not in \usage in documentation object 'changeDevSettings':
  'defaultsSettings'

Documented arguments not in \usage in documentation object 'checkMethod':
  'allowedMethod'

Documented arguments not in \usage in documentation object 'convertListToS4':
  'names'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'i_is_index':
  'max_length'

Documented arguments not in \usage in documentation object 'i_read_asd_spectra':
  'format'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/spflow.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/spGARCH.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'split_feasibility.Rd':
  'split_feasibility-package'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Feature Changes
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
Missing or unexported objects:
  'Matrix::crossprod' 'Matrix::tcrossprod'
Error(s) in re-building vignettes:
--- re-building 'basics.Rmd' using rmarkdown

Quitting from lines 194-195 [unnamed-chunk-16] (basics.Rmd)
Error: processing vignette 'basics.Rmd' failed with diagnostics:
'crossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'basics.Rmd'

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

Quitting from lines 371-372 [unnamed-chunk-33] (guide.Rmd)
Error: processing vignette 'guide.Rmd' failed with diagnostics:
'crossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'guide.Rmd'

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

SUMMARY: processing the following files failed:
  'basics.Rmd' 'guide.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs      1.6Mb
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'obis_search':
  'scientificname'

Documented arguments not in \usage in documentation object 'spocc_objects':
  'n'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'basketball_center_circle_fill':
  'linethickness'

Documented arguments not in \usage in documentation object 'basketball_free_throw_circle_dash':
  'end_angleThe'

Documented arguments not in \usage in documentation object 'basketball_painted_area':
  'free_throw_lane_boundary_line_thickness'

Documented arguments not in \usage in documentation object 'curling_features_set_colors':
  'sheet' 'ring_1' 'ring_2' 'ring_3'

Documented arguments not in \usage in documentation object 'football_field_border':
  'boundary_thickness'

Documented arguments not in \usage in documentation object 'football_field_border_outline':
  'boundary_thickness'

Documented arguments not in \usage in documentation object 'hockey_features_set_colors':
  'boards_color' 'center_line_color' 'blue_line_color'
  'goal_line_color' 'goalkeepers_restricted_area_color'
  'goal_crease_outline_color' 'goal_crease_fill_color'
  'referee_crease_color' 'center_faceoff_spot_color'
  'faceoff_spot_outer_ring_color' 'faceoff_spot_fill_color'
  'center_faceoff_circle_color' 'non_center_faceoff_circle_color'
  'faceoff_line_color' 'goal_color' 'goal_fill_color'

Documented arguments not in \usage in documentation object 'lacrosse_off_field_officials_box':
  'feature_thickness'

Documented arguments not in \usage in documentation object 'lacrosse_penalty_box_outline':
  'feature_thickness'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'checkFunEvalsDesignSize':
  'fun' 'upper'

Documented arguments not in \usage in documentation object 'print.spotBOModel':
  'object'

Documented arguments not in \usage in documentation object 'print.spotGaussianProcessModel':
  'object'

Documented arguments not in \usage in documentation object 'print.spotLOESS':
  'object'

Documented arguments not in \usage in documentation object 'print.spotLassoModel':
  'object'

Documented arguments not in \usage in documentation object 'print.spotLinearModel':
  'object'

Documented arguments not in \usage in documentation object 'print.spotRSM':
  'object'

Documented arguments not in \usage in documentation object 'print.spotRandomForest':
  'object'

Documented arguments not in \usage in documentation object 'print.spotRanger':
  'object'

Documented arguments not in \usage in documentation object 'print.spotSeverity':
  'object'

Documented arguments not in \usage in documentation object 'print.spotTreeModel':
  'object'

Documented arguments not in \usage in documentation object 'simulationSpectral':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/spsur.Rcheck/00install.out' for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
Running 'testthat.R' [94s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spsurvey)
  Loading required package: sf
  Linking to GEOS 3.11.2, GDAL 3.6.2, PROJ 9.2.0; sf_use_s2() is TRUE
  Loading required package: survey
  Loading required package: grid
  Loading required package: Matrix
  Loading required package: survival
  
  Attaching package: 'survey'
  
  The following object is masked from 'package:graphics':
  
      dotchart
  
  spsurvey version 5.0.0 introduced significant changes to the inputs and outputs of many functions. Please review the updated materials, vignettes, and documentation by visiting 
   https://cran.r-project.org/package=spsurvey
  > 
  > test_check("spsurvey")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 857 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cat_analysis.R:232:1'): (code run outside of `test_that()`) ────
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'as.matrix': 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─spsurvey::cat_analysis(...) at test-cat_analysis.R:232:0
    2. │ └─spsurvey:::category_est(...)
    3. │   ├─survey::svymean(...)
    4. │   └─survey:::svymean.pps(...)
    5. │     └─survey:::ppsvar(x * pweights/psum, design)
    6. │       └─survey:::htvar.matrix(...)
    7. │         └─base::apply(...)
    8. │           └─survey (local) FUN(newX[, i], ...)
    9. │             └─base::apply(...)
   10. │               └─survey (local) FUN(newX[, i], ...)
   11. │                 └─base::as.matrix(Matrix::crossprod(xicheck, Dcheck %*% xjcheck))
   12. └─base::.handleSimpleError(...)
   13.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 857 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Argument items with no description in Rd object 'sim.kong':
  'gamma' 'beta' 'design' 'rho' 'seed' 'impute' 'ppi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'squat-Ex.R' failed
The error most likely occurred in:

> ### Name: autoplot.prcomp_qts
> ### Title: Plot for 'prcomp_qts' objects
> ### Aliases: autoplot.prcomp_qts
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("ggplot2", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ df <- as_qts_sample(vespa64$igp[1:16])
+ res_pca <- prcomp(df)
+ 
+ # Plot the data points in a PC plane
+ # And color points according to a categorical variable
+ p <- ggplot2::autoplot(res_pca, what = "scores")
+ p + ggplot2::geom_point(ggplot2::aes(color = vespa64$V[1:16]))
+ ## Don't show: 
+ }) # examplesIf
> df <- as_qts_sample(vespa64$igp[1:16])
> res_pca <- prcomp(df)
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.3Mb
Documented arguments not in \usage in documentation object 'Expected time series dynamics':
  'logs2'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SRTsim.Rcheck/00install.out' for details.
Running 'spelling.R' [0s]
  Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(srvyr)
  
  Attaching package: 'srvyr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("srvyr")
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 400 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_as_survey_twophase.r:20:1'): (code run outside of `test_that()`) ──
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'as.matrix': 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─... %>% tibble::as_tibble() at test_as_survey_twophase.r:20:0
    2. ├─tibble::as_tibble(.)
    3. ├─stats::setNames(...)
    4. ├─dplyr::bind_cols(.)
    5. │ └─rlang::list2(...)
    6. ├─base::as.data.frame(svymean(~bili, d2pbc_survey))
    7. ├─survey::svymean(~bili, d2pbc_survey)
    8. ├─survey:::svymean.twophase2(~bili, d2pbc_survey)
    9. │ └─survey::twophase2var(x * pweights/psum, design)
   10. │   └─survey:::htvar.matrix(x, design$dcheck$full)
   11. │     └─base::apply(...)
   12. │       └─survey (local) FUN(newX[, i], ...)
   13. │         └─base::apply(...)
   14. │           └─survey (local) FUN(newX[, i], ...)
   15. │             └─base::as.matrix(Matrix::crossprod(xicheck, Dcheck %*% xjcheck))
   16. └─base::.handleSimpleError(...)
   17.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 400 ]
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SSBtools.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  13.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'namesMultiple':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Running examples in 'stablespec-Ex.R' failed
The error most likely occurred in:

> ### Name: getModelFitness
> ### Title: Scoring the given SEM models.
> ### Aliases: getModelFitness
> 
> ### ** Examples
> 
> the_data <- crossdata6V
> #assummed that variable 5 does not cause variables 1, 2, and 3
> models <- modelPop(nPop=5, numVar=6, longitudinal=FALSE,
+ consMatrix = matrix(c(5, 1, 5, 2, 5, 3), 3, 2, byrow=TRUE))
> 
> model_fitness <- getModelFitness(theData=the_data,
+ allModelString=models, numTime=1, longitudinal=FALSE,
+ co="covariance", mixture = FALSE)
Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'stack_predict':
  'type'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'connect,report_mig-method':
  'h' '...'

Documented arguments not in \usage in documentation object 'print,report_mig-method':
  'h'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'which_class':
  'character'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Missing or unexported object: 'Matrix::crossprod'
Running examples in 'stan4bart-Ex.R' failed
The error most likely occurred in:

> ### Name: stan4bart
> ### Title: Semiparametric Models Using Stan and BART
> ### Aliases: stan4bart
> 
> ### ** Examples
> 
> # simulate data (extension of Friedman MARS paper)
> # x consists of 10 variables, only first 5 matter
> # x_4 is linear
> f <- function(x)
+   10 * sin(pi * x[,1] * x[,2]) + 20 * (x[,3] - 0.5)^2 +
+       10 * x[,4] + 5 * x[,5]
> 
> set.seed(99)
> sigma <- 1.0
> 
> n <- 100
> n.g.1 <- 5L
> n.g.2 <- 8L
> 
> # sample observation level covariates and calculate marginal mean
> x <- matrix(runif(n * 10), n, 10)
> mu.bart  <- f(x) - 10 * x[,4]
> mu.fixef <- 10 * x[,4]
> 
> # varying intercepts and slopes for first grouping factor
> g.1 <- sample(n.g.1, n, replace = TRUE)
> Sigma.b.1 <- matrix(c(1.5^2, .2, .2, 1^2), 2)
> b.1 <- matrix(rnorm(2 * n.g.1), n.g.1) %*% chol(Sigma.b.1)
> 
> # varying intercepts for second grouping factor
> g.2 <- sample(n.g.2, n, replace = TRUE)
> Sigma.b.2 <- as.matrix(1.2)
> b.2 <- rnorm(n.g.2, 0, sqrt(Sigma.b.2))
> 
> mu.ranef <- b.1[g.1,1] + x[,4] * b.1[g.1,2] + b.2[g.2]
> 
> y <- mu.bart + mu.fixef + mu.ranef + rnorm(n, 0, sigma)
> 
> df <- data.frame(y, x, g.1, g.2)
> 
> fit <- stan4bart(
+     formula = y ~
+         X4 +                         # linear component ("fixef")
+         (1 + X4 | g.1) + (1 | g.2) + # multilevel ("ranef")
+         bart(. - g.1 - g.2 - X4),    # use bart for other variables
+     verbose = -1, # suppress ALL output
+     # low numbers for illustration
+     data = df,
+     chains = 1, iter = 10, bart_args = list(n.trees = 5))
> 
> # posterior means of individual expected values
> y.hat <- fitted(fit)
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    include  11.3Mb
GNU make is a SystemRequirements.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    To do
Package suggested but not available for checking: 'starsdata'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    1.7Mb
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'statcheck-package.Rd':
  '{statcheck}-package'
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.4Mb
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
Missing or unexported objects:
  'Matrix::crossprod' 'Matrix::tcrossprod'
Error(s) in re-building vignettes:
--- re-building 'Overview_HTP.Rmd' using rmarkdown

Quitting from lines 391-406 [fitPsHDMVator] (Overview_HTP.Rmd)
Error: processing vignette 'Overview_HTP.Rmd' failed with diagnostics:
'crossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'Overview_HTP.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in documentation object 'estEffsCPP':
  'y' 'w' 'x' 'ncores'

Documented arguments not in \usage in documentation object 'updateFA':
  'Y' 'WStart' 'm' 'PStart'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: 'networksis'
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.1Mb
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'INLA'
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/stevemisc.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Running examples in 'SticsRFiles-Ex.R' failed
The error most likely occurred in:

> ### Name: download_data
> ### Title: Download example USMs
> ### Aliases: download_data
> 
> ### ** Examples
> 
> 
> # Getting all data
> download_data()
trying URL 'https://github.com/SticsRPacks/data/archive/master.zip'
downloaded 985 KB

[1] "D:/temp/RtmpgvEAx8/data-master/study_case_1/V10.0"
> 
> download_data(example_dirs = "study_case_1")
trying URL 'https://github.com/SticsRPacks/data/archive/master.zip'
downloaded 161 KB

Warning in utils::download.file("https://github.com/SticsRPacks/data/archive/master.zip",  :
  URL 'https://codeload.github.com/SticsRPacks/data/zip/refs/heads/master': Timeout of 60 seconds was reached
Error in utils::download.file("https://github.com/SticsRPacks/data/archive/master.zip",  : 
  download from 'https://github.com/SticsRPacks/data/archive/master.zip' failed
Calls: download_data -> <Anonymous>
Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [134s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SticsRFiles)
  Learn SticsRFiles at: https://SticsRPacks.github.io/SticsRFiles
  > 
  > test_check("SticsRFiles")
  trying URL 'https://github.com/SticsRPacks/data/archive/master.zip'
  downloaded 91 KB
  
  trying URL 'https://github.com/SticsRPacks/data/archive/master.zip'
  downloaded 985 KB
  
  [ FAIL 1 | WARN 15 | SKIP 0 | PASS 249 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-get_obs.R:111:1'): (code run outside of `test_that()`) ─────────
  Error in `utils::download.file("https://github.com/SticsRPacks/data/archive/master.zip", 
      data_dir_zip)`: download from 'https://github.com/SticsRPacks/data/archive/master.zip' failed
  Backtrace:
      ▆
   1. └─SticsRFiles::download_data(...) at test-get_obs.R:111:0
   2.   └─utils::download.file(...)
  
  [ FAIL 1 | WARN 15 | SKIP 0 | PASS 249 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Running examples in 'stminsights-Ex.R' failed
The error most likely occurred in:

> ### Name: get_diag
> ### Title: computes stm model diagnostics
> ### Aliases: get_diag
> 
> ### ** Examples
> 
> 
> library(stm)
stm v1.3.6.1 successfully loaded. See ?stm for help. 
 Papers, resources, and other materials at structuraltopicmodel.com
> 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(ggplot2)
> library(quanteda)
Package version: 3.3.1
Unicode version: 13.0
ICU version: 69.1
Parallel computing: 2 of 96 threads used.
See https://quanteda.io for tutorials and examples.
> 
> # prepare data
> data <- corpus(gadarian, text_field = 'open.ended.response')
> docvars(data)$text <- as.character(data)
> 
> data <- tokens(data, remove_punct = TRUE) |>
+   tokens_wordstem() |>
+   tokens_remove(stopwords('english')) |> dfm() |>
+   dfm_trim(min_termfreq = 2)
> 
> out <- convert(data, to = 'stm')
> 
> # fit models
> gadarian_3 <- stm(documents = out$documents,
+                   vocab = out$vocab,
+                   data = out$meta,
+                   prevalence = ~ treatment + s(pid_rep),
+                   K = 3,
+                   max.em.its = 1, # reduce computation time for example
+                   verbose = FALSE)
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Missing or unexported object: 'Matrix::crossprod'
Running examples in 'stm-Ex.R' failed
The error most likely occurred in:

> ### Name: alignCorpus
> ### Title: Align the vocabulary of a new corpus to an old corpus
> ### Aliases: alignCorpus
> 
> ### ** Examples
> 
> #we process an original set that is just the first 100 documents
> temp<-textProcessor(documents=gadarian$open.ended.response[1:100],metadata=gadarian[1:100,])
Building corpus... 
Converting to Lower Case... 
Removing punctuation... 
Removing stopwords... 
Removing numbers... 
Stemming... 
Creating Output... 
> out <- prepDocuments(temp$documents, temp$vocab, temp$meta)
Removing 329 of 512 terms (329 of 1139 tokens) due to frequency 
Removing 2 Documents with No Words 
Your corpus now has 98 documents, 183 terms and 810 tokens.> set.seed(02138)
> #Maximum EM its is set low to make this run fast, run models to convergence!
> mod.out <- stm(out$documents, out$vocab, 3, prevalence=~treatment + s(pid_rep), 
+               data=out$meta, max.em.its=5)
Beginning Spectral Initialization 
	 Calculating the gram matrix...
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Argument items with no description in Rd object 'd.sum.of.mixtures.EXPLN':
  'p.vector'
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object 'strategicplayers-package':
  \details: '...o use the package, including the most important functions ~~'
  \references: '~~ Literature or other references for background information ~~'
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/STraTUS.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/STREAK.Rcheck/00install.out' for details.
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'get_groups':
  'groups'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'STRaitRazoR'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/STRMPS.Rcheck/00install.out' for details.
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'StructFDR-package.Rd':
  'TreeFDR-package'
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'size.penalize':
  'size.penalize'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'subsamp':
  'x:' 'y:' 's:' 'm:' 'qnum:' 'wplot:'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SubtypeDrug.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.3Mb
Auto-generated content requiring editing in Rd object 'supcluster-package':
  \references: '~~ Literature or other references for background information ~~'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'extraTrees'
Unknown package 'extraTrees' in Rd xrefs
Package suggested but not available for checking: 'extraTrees'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'check_package':
  'X'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/surface.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'INLA', 'gpclib'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.2Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
Running examples in 'SurveyCC-Ex.R' failed
The error most likely occurred in:

> ### Name: surveycc
> ### Title: Canonical correlation analysis for complex survey data
> ### Aliases: surveycc
> 
> ### ** Examples
> 
> # PATH example
> design_object <-
+  survey::svrepdesign(
+  id = ~PERSONID,
+  weights = ~R01_A_PWGT,
+  repweights = "R01_A_PWGT[1-9]+",
+  type = "Fay",
+  rho = 0.3,
+  data=reducedPATHdata,
+  mse = TRUE
+  )
> var.x <- c("R01_AC1022", "R01_AE1022", "R01_AG1022CG")
> var.y <- c("R01_AX0075", "R01_AX0076")
> howmany <- 2
> dim1 <- 1
> dim2 <- 2
> surveycc(design_object, var.x, var.y, howmany = howmany,
+   dim1 = dim1, dim2 = dim2, selection = "x")
Error in crossprod(x * sqrt(scale)) : 
  "crossprod" is not a BUILTIN function
Calls: surveycc ... multistage -> onestage -> tapply -> lapply -> FUN -> onestrat
Execution halted
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::crossprod'
Package suggested but not available for checking: 'gurobi'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/surveyvoi.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
Package suggested but not available for checking: 'distr6'
Unknown package 'distr6' in Rd xrefs
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.9Mb
Specified C++11: please drop specification unless essential
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Unknown package 'survJamda' in Rd xrefs
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/susieR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
checkRd: (-1) diabetes.Rd:18: Escaped LaTeX specials: \^
Running examples in 'svrep-Ex.R' failed
The error most likely occurred in:

> ### Name: make_fays_gen_rep_factors
> ### Title: Form replication factors using Fay's generalized replication
> ###   method
> ### Aliases: make_fays_gen_rep_factors
> 
> ### ** Examples
> 
>   library(survey)
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

> 
> # Load an example dataset that uses unequal probability sampling ----
>   data('election', package = 'survey')
> 
> # Create matrix to represent the Horvitz-Thompson estimator as a quadratic form ----
>   n <- nrow(election_pps)
>   pi <- election_jointprob
>   horvitz_thompson_matrix <- matrix(nrow = n, ncol = n)
>   for (i in seq_len(n)) {
+     for (j in seq_len(n)) {
+       horvitz_thompson_matrix[i,j] <- 1 - (pi[i,i] * pi[j,j])/pi[i,j]
+     }
+   }
> 
>   ## Equivalently:
> 
>   horvitz_thompson_matrix <- make_quad_form_matrix(
+     variance_estimator = "Horvitz-Thompson",
+     joint_probs = election_jointprob
+   )
> 
> # Make generalized replication adjustment factors ----
> 
>   adjustment_factors <- make_fays_gen_rep_factors(
+     Sigma = horvitz_thompson_matrix,
+     max_replicates = 50
+   )
>   attr(adjustment_factors, 'scale')
[1] 1
> 
> # Compute the Horvitz-Thompson estimate and the replication estimate
> 
> ht_estimate <- svydesign(data = election_pps, ids = ~ 1,
+                          prob = diag(election_jointprob),
+                          pps = ppsmat(election_jointprob)) |>
+   svytotal(x = ~ Kerry)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': 'crossprod' is not an exported object from 'namespace:Matrix'
Calls: svytotal ... apply -> FUN -> as.matrix -> .handleSimpleError -> h
Execution halted
Error(s) in re-building vignettes:
--- re-building 'bootstrap-replicates.Rmd' using rmarkdown

Quitting from lines 123-135 [unnamed-chunk-3] (bootstrap-replicates.Rmd)
Error: processing vignette 'bootstrap-replicates.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.matrix': 'crossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'bootstrap-replicates.Rmd'

--- re-building 'nonresponse-adjustments.Rmd' using rmarkdown
--- finished re-building 'nonresponse-adjustments.Rmd'

--- re-building 'sample-based-calibration.Rmd' using rmarkdown
--- finished re-building 'sample-based-calibration.Rmd'

--- re-building 'two-phase-sampling.Rmd' using rmarkdown
--- finished re-building 'two-phase-sampling.Rmd'

SUMMARY: processing the following file failed:
  'bootstrap-replicates.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/svs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'swephRdata'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'syncrng-package.Rd':
  'syncrng-package'
Error(s) in re-building vignettes:
--- re-building 'SynDI-example-binary.Rmd' using knitr

Quitting from lines 35-43 [unnamed-chunk-3] (SynDI-example-binary.Rmd)
Error: processing vignette 'SynDI-example-binary.Rmd' failed with diagnostics:
package or namespace load failed for 'arm':
 objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
--- failed re-building 'SynDI-example-binary.Rmd'

--- re-building 'SynDI-example-continuous.Rmd' using knitr

Quitting from lines 35-43 [unnamed-chunk-3] (SynDI-example-continuous.Rmd)
Error: processing vignette 'SynDI-example-continuous.Rmd' failed with diagnostics:
package or namespace load failed for 'arm':
 objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
--- failed re-building 'SynDI-example-continuous.Rmd'

SUMMARY: processing the following files failed:
  'SynDI-example-binary.Rmd' 'SynDI-example-continuous.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'dingemanse-data-example.Rmd' using rmarkdown

Quitting from lines 41-44 [download_data] (dingemanse-data-example.Rmd)
Error: processing vignette 'dingemanse-data-example.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/mdingemanse/colouredvowels/master/BRM_colouredvowels_voweldata.csv'
--- failed re-building 'dingemanse-data-example.Rmd'

--- re-building 'quick-start.Rmd' using rmarkdown
--- finished re-building 'quick-start.Rmd'

--- re-building 'synr-creategroup.Rmd' using rmarkdown
--- finished re-building 'synr-creategroup.Rmd'

--- re-building 'synr-tutorial.Rmd' using rmarkdown
--- finished re-building 'synr-tutorial.Rmd'

--- re-building 'validate-data.Rmd' using rmarkdown
--- finished re-building 'validate-data.Rmd'

SUMMARY: processing the following file failed:
  'dingemanse-data-example.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'unix'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'table_params_circle':
  'd'

Documented arguments not in \usage in documentation object 'table_params_rect':
  'd' 'scale_breaks' 'r_max'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'plot.prEntries':
  'plot.margin' 'sizeAdjust'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'designMatrices':
  'print.designMatrices'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Missing or unexported object: 'Matrix::tcrossprod'
Error(s) in re-building vignettes:
--- re-building 'Correlation.Rmd' using rmarkdown
--- finished re-building 'Correlation.Rmd'

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

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

Quitting from lines 53-54 [Function call] (Example_Walkthrough.Rmd)
Error: processing vignette 'Example_Walkthrough.Rmd' failed with diagnostics:
'tcrossprod' is not an exported object from 'namespace:Matrix'
--- failed re-building 'Example_Walkthrough.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tapnet.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tashudata'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'default_db_ref':
  'name' 'url' 'desc' 'id_regex'

Documented arguments not in \usage in documentation object 'limited_print':
  'trunc'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tbm.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/TBRDist.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/TCA.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) R2txt.Rd:164: Escaped LaTeX specials: \#
checkRd: (-1) bct.Rd:18: Escaped LaTeX specials: \^
checkRd: (-1) bct.Rd:19: Escaped LaTeX specials: \^
checkRd: (-1) ineq.Rd:10: Escaped LaTeX specials: \&
checkRd: (-1) put.points.demo.Rd:39: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:10: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:31: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       3.7Mb
    libs      1.1Mb
    telemac   1.0Mb
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'extract_sptensor':
  'idxmat'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 100.6Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    gdal   2.9Mb
    libs  86.0Mb
    proj   8.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tessellation.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.0Mb
    tessdata  14.0Mb
Package suggested but not available for checking: 'gurobi'
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(TestDimorph)
  > if (requireNamespace("testthat", quietly = TRUE)) {
  +   library("testthat")
  + } else {
  +   message("'testthat' not available")
  + }
  > test_check("TestDimorph")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-extract_sum.R:2:3'): extract_sum ───────────────────────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─testthat::expect_true(...) at test-extract_sum.R:2:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─TestDimorph::extract_sum(Howells, test = "multi")
   5. │ └─TestDimorph:::pooled_cov(as.matrix(X), ina)
   6. └─base::loadNamespace(x)
   7.   └─base::namespaceImportFrom(...)
   8.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'Examples.Rmd' using rmarkdown

Quitting from lines 56-64 [Table 3] (Examples.Rmd)
Error: processing vignette 'Examples.Rmd' failed with diagnostics:
object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'Examples.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'safe_digest':
  'filename'

Documented arguments not in \usage in documentation object 'with_mock':
  '.local_env'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'CompileLatexDir':
  'engine:' 'compile.dir:'

Documented arguments not in \usage in documentation object 'GetLayerSampleIndexes':
  'NamesOfListToSample' 'isRandomized'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/text2map.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.0Mb
    libs   1.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/TextForecast.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/textplot.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Unknown package 'textreadr' in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in documentation object 'tframe.timeSeries':
  'tbind.timeSeries'

Objects in \usage without \alias in documentation object 'tframe.tis':
  'tfstart.tis'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
Error(s) in re-building vignettes:
--- re-building 'blood_loss_report.Rnw' using knitr

Quitting from lines 30-131 [setup] (blood_loss_report.Rnw)
Error: processing vignette 'blood_loss_report.Rnw' failed with diagnostics:
package 'mlt' could not be loaded
--- failed re-building 'blood_loss_report.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    data   3.0Mb
Documented arguments not in \usage in documentation object 'witcherMap':
  'palettes'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'poisson_likelihood':
  'rate_exp' 'rate_ref' 'rate_pla'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'hclust_fit':
  'h'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'tidyfit-Ex.R' failed
The error most likely occurred in:

> ### Name: .fit.bayes
> ### Title: Bayesian generalized linear regression for 'tidyfit'
> ### Aliases: .fit.bayes
> 
> ### ** Examples
> 
> # Load data
> data <- tidyfit::Factor_Industry_Returns
> 
> # Stand-alone function
> fit <- m("bayes", Return ~ ., data)
Error in `purrr::map()`:
ℹ In index: 1.
Caused by error:
! objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
Backtrace:
     ▆
  1. ├─tidyfit::m("bayes", Return ~ ., data)
  2. │ └─purrr::map(mods$model_object, function(mod) mod$fit(data))
  3. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  4. │     ├─purrr:::with_indexed_errors(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     ├─purrr:::call_with_cleanup(...)
  7. │     └─tidyfit (local) .f(.x[[i]], ...)
  8. │       └─mod$fit(data)
  9. │         ├─tidyfit:::.fit(self, ...)
 10. │         └─tidyfit:::.fit.bayes(self, ...)
 11. │           ├─names(self$args) %in% methods::formalArgs(arm::bayesglm)
 12. │           └─methods::formalArgs(arm::bayesglm)
 13. │             └─base::formals(def, envir = parent.frame())
 14. ├─base::loadNamespace(x)
 15. │ └─base::namespaceImportFrom(...)
 16. │   └─base::importIntoEnv(impenv, impnames, ns, impvars)
 17. │     └─base::stop(...)
 18. └─base::.handleSimpleError(...)
 19.   └─purrr (local) h(simpleError(msg, call))
 20.     └─cli::cli_abort(...)
 21.       └─rlang::abort(...)
Execution halted
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'gate_interactive_chr_int':
  'gate_list'

Documented arguments not in \usage in documentation object 'gate_programmatic':
  '...'

Documented arguments not in \usage in documentation object 'gate_programmatic_chr_int':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
Error(s) in re-building vignettes:
--- re-building 'TQ00-introduction-to-tidyquant.Rmd' using rmarkdown
--- finished re-building 'TQ00-introduction-to-tidyquant.Rmd'

--- re-building 'TQ01-core-functions-in-tidyquant.Rmd' using rmarkdown
--- finished re-building 'TQ01-core-functions-in-tidyquant.Rmd'

--- re-building 'TQ02-quant-integrations-in-tidyquant.Rmd' using rmarkdown

Quitting from lines 476-482 [unnamed-chunk-27] (TQ02-quant-integrations-in-tidyquant.Rmd)
Error: processing vignette 'TQ02-quant-integrations-in-tidyquant.Rmd' failed with diagnostics:
Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error:
! object 'MA' not found
--- failed re-building 'TQ02-quant-integrations-in-tidyquant.Rmd'

--- re-building 'TQ03-scaling-and-modeling-with-tidyquant.Rmd' using rmarkdown
--- finished re-building 'TQ03-scaling-and-modeling-with-tidyquant.Rmd'

--- re-building 'TQ04-charting-with-tidyquant.Rmd' using rmarkdown
--- finished re-building 'TQ04-charting-with-tidyquant.Rmd'

--- re-building 'TQ05-performance-analysis-with-tidyquant.Rmd' using rmarkdown

Quitting from lines 272-279 [unnamed-chunk-17] (TQ05-performance-analysis-with-tidyquant.Rmd)
Error: processing vignette 'TQ05-performance-analysis-with-tidyquant.Rmd' failed with diagnostics:
Can't recycle `..1` (size 2) to match `..2` (size 3).
--- failed re-building 'TQ05-performance-analysis-with-tidyquant.Rmd'

--- re-building 'TQ06-excel-in-r.Rmd' using rmarkdown
--- finished re-building 'TQ06-excel-in-r.Rmd'

SUMMARY: processing the following files failed:
  'TQ02-quant-integrations-in-tidyquant.Rmd'
  'TQ05-performance-analysis-with-tidyquant.Rmd'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'deprecated-se':
  'expand_cols'

Documented arguments not in \usage in documentation object 'tidyr_legacy':
  'nm'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'vars_select':
  'args'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tidyseurat.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  
  Attaching package: 'NLP'
  
  The following object is masked from 'package:ggplot2':
  
      annotate
  
  stm v1.3.6.1 successfully loaded. See ?stm for help. 
   Papers, resources, and other materials at structuraltopicmodel.com
  [ FAIL 1 | WARN 65 | SKIP 7 | PASS 254 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-reorder-within.R:29:3', 'test-reorder-within.R:47:3',
    'test-reorder-within.R:64:3', 'test-unnest-tokens.R:53:3',
    'test-unnest-tokens.R:203:3', 'test-unnest-tokens.R:442:3',
    'test-unnest_tweet.R:6:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-stm-tidiers.R:11:1'): (code run outside of `test_that()`) ──────
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─stm::stm(m, seed = 1234, K = 3, verbose = FALSE) at test-stm-tidiers.R:11:0
   2.   └─stm:::stm.control(documents, vocab, settings, model)
   3.     └─stm:::stm.init(documents, settings)
   4.       └─stm:::gram(mat)
  
  [ FAIL 1 | WARN 65 | SKIP 7 | PASS 254 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'freq.Rmd' using rmarkdown
--- finished re-building 'freq.Rmd'

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

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

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

Quitting from lines 280-323 [unnamed-chunk-13] (tidytlg.Rmd)
Error: processing vignette 'tidytlg.Rmd' failed with diagnostics:
cannot open the connection to 'https://github.com/phuse-org/TestDataFactory/raw/main/Updated/TDF_ADaM/adsl.xpt'
--- failed re-building 'tidytlg.Rmd'

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   4.5Mb
Error(s) in re-building vignettes:
--- re-building 'frequency.Rmd' using rmarkdown
--- finished re-building 'frequency.Rmd'

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

Quitting from lines 136-143 [unnamed-chunk-7] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection to 'https://bit.ly/catalogs-csv'
--- failed re-building 'introduction.Rmd'

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

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

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  common.c:36:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/tiff.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tigger.Rcheck/00install.out' for details.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object 'timeperiodsR-package':
  \details: '...o use the package, including the most important functions ~~'
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'timeSeq_1.0.4-package.Rd':
  'timeSeq_1.0.4-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
620 +38.7776249 -75.3120536 POLYGON ((-75.31274 38.7775...
621 +38.7365038 -75.2114740 POLYGON ((-75.21206 38.7365...
622 +38.4885724 -75.0755628 POLYGON ((-75.07653 38.4883...
623 +38.4558690 -75.0561527 POLYGON ((-75.0588 38.45432...
624 +38.5496289 -75.0663459 POLYGON ((-75.07366 38.5465...
625 +38.5439409 -75.0777788 POLYGON ((-75.0794 38.54312...
626 +38.5043250 -75.0699328 POLYGON ((-75.07329 38.5048...
627 +38.5594378 -75.0678318 POLYGON ((-75.06949 38.5595...
628 +38.5755845 -75.1595155 POLYGON ((-75.16268 38.5798...
629 +38.5704540 -75.1982985 POLYGON ((-75.19982 38.5689...
630 +38.5861347 -75.2223496 POLYGON ((-75.22585 38.5865...
631 +38.4560432 -75.1477660 POLYGON ((-75.1485 38.456, ...
632 +38.5234542 -75.1070409 POLYGON ((-75.10756 38.5232...
> 
> 
> 
> cleanEx()
> nameEx("tt_block_groups")
> ### * tt_block_groups
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: tt_block_groups
> ### Title: Download TIGER shapes for block groups
> ### Aliases: tt_block_groups
> 
> ### ** Examples
> 
> # Wrapped in try due to false positive 304 errors
> try(tt_block_groups(state = "DE", county = "001"))
======== End of example output (where/before crash/hang up occured ?) ========
Specified C++14: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:131:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:334:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:453:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:471:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:496:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:497:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:509:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:522:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:1053:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:93:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:94:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/tkrplot.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    examples  12.6Mb
    include    3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/TML.Rcheck/00install.out' for details.
Invalid package aliases in Rd file 'tm.plugin.alceste-package.Rd':
  'tm.plugin.europresse-package'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'TNRS_core':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> flush(stderr()); flush(stdout())
> 
> ### Name: TNRS_version
> ### Title: Get metadata on current TNRS version
> ### Aliases: TNRS_version
> 
> ### ** Examples
> 
> {
+   TNRS_version_metadata <- TNRS_version()
+ }
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  0.55 0.06 2.64 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data-tables   1.4Mb
    doc           1.9Mb
    help          1.2Mb
'LazyData' is specified without a 'data' directory
Running examples in 'topicmodels.etm-Ex.R' failed
The error most likely occurred in:

> ### Name: ETM
> ### Title: Topic Modelling in Semantic Embedding Spaces
> ### Aliases: ETM
> 
> ### ** Examples
> 
> library(torch)
> library(topicmodels.etm)
> library(word2vec)
> library(udpipe)
Error: package or namespace load failed for 'udpipe':
 object 'crossprod' is not exported by 'namespace:Matrix'
Execution halted
Package suggested but not available for checking: 'corpus.JSS.papers'
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/topologyGSA.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    R         5.5Mb
    help      1.6Mb
    include   3.4Mb
    libs     17.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'toscaData'
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Documented arguments not in \usage in documentation object 'createLink':
  'hits'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'demo.Rmd' using rmarkdown

Quitting from lines 106-110 [unnamed-chunk-7] (demo.Rmd)
Error: processing vignette 'demo.Rmd' failed with diagnostics:
object 'crossprod' is not exported by 'namespace:Matrix'
--- failed re-building 'demo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
Argument items with no description in Rd object 'noblabrams':
  'prior' 'change'
Argument items with no description in Rd object 'absoluteIncreaseALL':
  'storedev' '\dots'
Argument items with no description in Rd object 'boundaryLineALL':
  '\dots'
Argument items with no description in Rd object 'growthAveragingALL':
  '\dots'
Argument items with no description in Rd object 'plotFirstYears':
  '\dots'
Argument items with no description in Rd object 'plotRelease':
  '\dots'
Argument items with no description in Rd object 'splechtnaALL':
  '\dots'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taxidata'
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'seqimplic':
  'ylim'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tramME.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tramnet.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tram.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tramvs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in documentation object 'transport-internal':
  'gif.generate' 'plot_pgrid_wpp'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR'
Documented arguments not in \usage in documentation object 'clean_data':
  'a'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Documented arguments not in \usage in documentation object 'correct_continuous':
  'x'

Documented arguments not in \usage in documentation object 'tc_correlation':
  'p'

Documented arguments not in \usage in documentation object 'tc_efunc':
  'p'

Documented arguments not in \usage in documentation object 'tc_mfunc':
  'p'

Documented arguments not in \usage in documentation object 'tc_response':
  'p'

Documented arguments not in \usage in documentation object 'truncate_input':
  'moving'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/treedata.table.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/treediff.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'TreeDistData'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/TreeDist.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug fixes
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object 'treemisc-package':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '## Optional simple examples of the most important functions ...'
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/TreeSearch.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/TreeSimGM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/TreeSim.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/treespace.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/treestartr.Rcheck/00install.out' for details.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ##D 
> ##D # Content for the new card
> ##D payload = list(
> ##D   id = cid,
> ##D   name = "A new card name",
> ##D   desc = "Description - updated by trelloR",
> ##D   pos = "top" #put card on the top of a list
> ##D )
> ##D 
> ##D # Update card's name, descriptionand position
> ##D update_resource("card", id = cid, body = payload, token = token)
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.4 0.11 2.88 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/trendeval.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/trending.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'TRexSelector_usage_and_simulations.Rmd' using rmarkdown
Could not fetch http://www.zotero.org/styles/institute-of-mathematical-statistics
HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/institute-of-mathematical-statistics"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (ConnectionFailure user error (Network.Socket.gai_strerror not supported: 11002))
Error: processing vignette 'TRexSelector_usage_and_simulations.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building 'TRexSelector_usage_and_simulations.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    doc       1.3Mb
    extdata  14.8Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'check_variables':
  'ncol'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/trtf.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'log2console'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tsapp.Rcheck/00install.out' for details.
Documented arguments not in \usage in documentation object 'dvinecopula_objective':
  'udata'

Documented arguments not in \usage in documentation object 'wobjective':
  'vt'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Objects in \usage without \alias in documentation object 'nlar.struct':
  'getNUsed'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'tsibble-vctrs':
  'vec_ptype2.tbl_ts' 'vec_cast.tbl_ts' 'vec_cast.yearmonth'
  'vec_ptype2.yearmonth' 'vec_cast.yearquarter'
  'vec_ptype2.yearquarter' 'vec_cast.yearweek' 'vec_ptype2.yearweek'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'tsoutliers-package.Rd':
  'tsouliers-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Invalid package aliases in Rd file 'TTAinterface-package.Rd':
  'TTAinterface-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'Matrix::crossprod'
Running examples in 'tvReg-Ex.R' failed
The error most likely occurred in:

> ### Name: forecast
> ### Title: Forecast Methods for Objects in tvReg.
> ### Aliases: forecast forecast.tvlm forecast.tvar forecast.tvvar
> ###   forecast.tvsure forecast.tvplm
> 
> ### ** Examples
> 
> data("RV")
> RV2 <- head(RV, 2001)
> TVHAR <- tvLM (RV ~ RV_lag + RV_week + RV_month, data = RV2, bw = 20)
> newdata <- cbind(RV$RV_lag[2002:2004], RV$RV_week[2002:2004],
+               RV$RV_month[2002:2004])
> forecast(TVHAR, newdata, n.ahead = 3)
[1] 1.820324e-05 1.930130e-05 2.573088e-05
> 
> 
> data("RV")
> exogen = RV[1:2001, c("RV_week", "RV_month")]
> TVHAR2 <- tvAR(RV$RV_lag[1:2001], p = 1, exogen = exogen, bw = 20)
> newexogen <- RV[2002:2004, c("RV_week", "RV_month")]
> forecast(TVHAR2, n.ahead = 3, newexogen = newexogen)
[1] 1.663144e-05 1.630848e-05 2.174843e-05
> 
> data(usmacro, package = "bvarsv")
> tvVAR.fit <- tvVAR(usmacro, p = 6, type = "const", bw = c(1.8, 20, 20))
> forecast(tvVAR.fit, n.ahead = 10)
           inf      une      tbi
 [1,] 2.296376 5.130155 2.985502
 [2,] 2.288106 5.191209 2.873162
 [3,] 2.249695 5.112356 2.524628
 [4,] 2.161933 4.939517 2.307814
 [5,] 2.167527 4.787522 2.584394
 [6,] 2.245035 4.685216 2.833504
 [7,] 2.374512 4.631450 2.895080
 [8,] 2.570610 4.592054 2.980562
 [9,] 2.769433 4.556460 3.120611
[10,] 2.962495 4.537426 3.385132
> 
> data("Kmenta", package = "systemfit")
> eqDemand <- consump ~ price + income
> eqSupply <- consump ~ price + farmPrice 
> system <- list(demand = eqDemand, supply = eqSupply)
> tvOLS.fit <- tvSURE(system, data = Kmenta, est = "ll", bw = c(1.5, 1.5))
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) lindner.Rd:44: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/twosigma.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'sl3'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/txshift.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    ubinc   2.0Mb
Documented arguments not in \usage in documentation object 'generate_parameter':
  'SIMINT_PARAMETERS_TV' 'SIMINT_PARAMETERS_IIV_VALUE'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.0Mb
    libs   4.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/udpipe.Rcheck/00install.out' for details.
Running examples in 'ufs-Ex.R' failed
The error most likely occurred in:

> ### Name: zotero_nr_of_items
> ### Title: Get number of items in a public Zotero group
> ### Aliases: zotero_nr_of_items
> 
> ### ** Examples
> 
> zotero_nr_of_items(2425237);
Warning in readLines(bibCon, warn = FALSE) :
  URL 'https://api.zotero.org/groups/2425237/items?format=keys': status was 'Couldn't resolve host name'
Error in readLines(bibCon, warn = FALSE) : 
  cannot open the connection to 'https://api.zotero.org/groups/2425237/items?format=keys'
Calls: zotero_nr_of_items -> readLines
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'HC':
  'X' 'K'
Argument items with no description in Rd object 'KA':
  'X' 'K' 'distancemetric'
Argument items with no description in Rd object 'SOMs':
  'X' 'K' 'topo' 'rlen' 'alpha' 'n.hood'
Argument items with no description in Rd object 'binarise':
  'U' 'K' 'technique' 'parameter'
Argument items with no description in Rd object 'closestToSquareFactors':
  'n'
Argument items with no description in Rd object 'clustDist':
  'U1' 'U2' 'X' 'criterion'
Argument items with no description in Rd object 'clustVec2partMat':
  'C'
Argument items with no description in Rd object 'clusterDataset':
  'X' 'K' 'D' 'methods'
Argument items with no description in Rd object 'factors':
  'n' 'primeonly'
Argument items with no description in Rd object 'fixnans':
  'X' 'type'
Argument items with no description in Rd object 'fuzzystretch':
  'X' 'x0'
Argument items with no description in Rd object 'generateCoPaM':
  'U' 'relabel_technique' 'w' 'X' 'distCriterion' 'K' 'GDM'
Argument items with no description in Rd object 'isValidBPM':
  'U'
Argument items with no description in Rd object 'isempty':
  'X'
Argument items with no description in Rd object 'isnullorempty':
  'X'
Argument items with no description in Rd object 'kmeansKA':
  'X' 'K' 'distancemetric' 'iter.max' 'nstart' 'algorithm' 'trace'
Argument items with no description in Rd object 'mnplots':
  'Vmse' 'mseCache' 'subplotdim' 'subplotind' 'minimiseDistance'
Argument items with no description in Rd object 'mseclusters':
  'X' 'B' 'normalise'
Argument items with no description in Rd object 'normaliseMatrix':
  'X' 'type'
Argument items with no description in Rd object 'partMat2clustVec':
  'U' 'skipValidity'
Argument items with no description in Rd object 'permutations':
  'n'
Argument items with no description in Rd object 'relabelClusts':
  'ref' 'input' 'technique' 'X' 'distCriterion'
Documented arguments not in \usage in documentation object 'sqrtm':
  'A'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  'ungroup.Rd'
Documented arguments not in \usage in documentation object 'MortSmooth_tpower':
  'vector'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/UniprotR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'as.character.bullet':
  'pre'

Documented arguments not in \usage in documentation object 'capture_output':
  'a'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.4Mb
    libs  14.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'USA.state.boundaries.data'
installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Documented arguments not in \usage in documentation object 'use_course_details':
  'destdir' 'zipfile'

Documented arguments not in \usage in documentation object 'write-this':
  'contents'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.2Mb
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checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
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installed size is  7.0Mb
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'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/utr.annotation.Rcheck/00install.out' for details.
Found the following significant warnings:
  randutils.c:60:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
installed size is 17.2Mb
  sub-directories of 1Mb or more:
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    libs  15.3Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
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Rd files without \alias:
  'valaddin.Rd'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/VALERIE.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object '.PKGOPT':
  'varlist:'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/valr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/vampyr.Rcheck/00install.out' for details.
installed size is 97.1Mb
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    gdal      2.9Mb
    libs     81.9Mb
    proj      8.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
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No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
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    doc   7.4Mb
Documented arguments not in \usage in documentation object 'vctrs-conditions':
  'subclass'

Documented arguments not in \usage in documentation object 'vec_as_subscript':
  'location'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'syntab':
  'print.syntab'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'vein-deprecated':
  'object'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
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checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
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checkRd: (-1) checkTS.VGAMextra.Rd:176: Escaped LaTeX specials: \&
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  sub-directories of 1Mb or more:
    R      4.1Mb
    help   2.9Mb
Missing link or links in documentation object 'profilevglm.Rd':
  '[MASS]{plot.profile}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Argument items with no description in Rd object 'learnPartitionWithLLR':
  'type' 'procedure' 'ql' 'qq' 'BinaryLearningProcedure'
Argument items with no description in Rd object 'plotClassifRule':
  'object'
Documented arguments not in \usage in documentation object 'boxplot_VICI':
  'res_2plot'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Vicus.Rcheck/00install.out' for details.
Documented arguments not in \usage in documentation object 'draw_map_shiny':
  'rigth.lim'

Documented arguments not in \usage in documentation object 'map_summary':
  'rigth.lim'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.2Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    NEW FEATURES
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/VIRF.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Documented arguments not in \usage in documentation object 'insert_preview':
  'input'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     19.1Mb
Documented arguments not in \usage in documentation object 'cpp_vol2bird_version':
  'path'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object 'blendColor':
  'color' 'percent'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
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Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(VSdecomp)
  > 
  > test_check("VSdecomp")
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 5 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • cran_skip is TRUE (5): 'test_skewness_functions.R:54:3',
    'test_skewness_functions.R:77:3', 'test_skewness_functions.R:101:3',
    'test_variance_functions.R:41:3', 'test_variance_functions.R:62:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_linear_projection.R:14:1'): (code run outside of `test_that()`) ──
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─VSdecomp::linear_projection(...) at test_linear_projection.R:14:0
   2. │ └─VSdecomp:::get_comp(dep_var, X.list, data[ind, ], wgt[ind])
   3. │   └─VSdecomp:::get_fe_terms(dep_var, all_x, are_factors, data, wgt)
   4. └─base::loadNamespace(x)
   5.   └─base::namespaceImportFrom(...)
   6.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 5 ]
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/VSOLassoBag.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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No news entries found.
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'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'get.wal.mipmap.heights':
  'height_mm'

Documented arguments not in \usage in documentation object 'get.wal.mipmap.widths':
  'width_mm'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Documented arguments not in \usage in documentation object 'WaveDjF':
  'y_fft'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Auto-generated content requiring editing in Rd object 'maxithresh':
  \details: '~~ If necessary, more details than the description above ~~'
  \arguments: data: '~~Describe \code{data} here~~'
  \arguments: g: '~~Describe \code{g} here~~'
  \arguments: L: '~~Describe \code{L} here~~'
  \arguments: F: '~~Describe \code{F} here~~'
  \arguments: eta: '~~Describe \code{eta} here~~'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'train_spectra':
  'save.model' 'vector.input'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
1 unsystematic_mse standard        23.6
> ww_systematic_rmse(example_df, x, y)
# A tibble: 1 × 3
  .metric         .estimator .estimate
  <chr>           <chr>          <dbl>
1 systematic_rmse standard       0.473
> ww_unsystematic_rmse(example_df, x, y)
# A tibble: 1 × 3
  .metric           .estimator .estimate
  <chr>             <chr>          <dbl>
1 unsystematic_rmse standard        4.86
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  12.88 0.91 13.78 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Invalid package aliases in Rd file 'wce-package.Rd':
  'wce-package'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'prepr'
Problems with news in 'NEWS.md':
No news entries found.
Argument items with no description in Rd object 'plotByRate':
  'baseTimeCol' 'baseDataCol' 'baseBaseRateCol'
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
Documented arguments not in \usage in documentation object 'read_img':
  'imgfile'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Invalid package aliases in Rd file 'print.webpower.Rd':
  'print.webpower-package'
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object 'zdifference_ordinal':
  'na.rm'
Missing or unexported objects:
  'Matrix::crossprod' 'Matrix::tcrossprod'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/wfe.Rcheck/00install.out' for details.
Argument items with no description in Rd object 'sampledHierarchicalConsensusModules':
  'consensusTOMFilePattern'
S3 methods shown with full name in documentation object 'QIC.gee':
  'QIC.gee'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Package suggested but not available for checking: 'anomalize'
Documented arguments not in \usage in documentation object 'remove_empty':
  'quiet'

Documented arguments not in \usage in documentation object 'undoHistory':
  'class' 'btn_class' 'back_text' 'fwd_text' 'back_title' 'fwd_title'
  'back_icon' 'fwd_icon'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'displayDataTable':
  'id'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/windex.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'WormTensor.Rmd' using rmarkdown
trying URL 'https://figshare.com/ndownloader/files/35963780'

Quitting from lines 39-40 [worm_download] (WormTensor.Rmd)
Error: processing vignette 'WormTensor.Rmd' failed with diagnostics:
cannot open URL 'https://figshare.com/ndownloader/files/35963780'
--- failed re-building 'WormTensor.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'new_givens_path':
  'generate'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'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
Malformed Title field: should not end in a period.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'sample_me':
  'middle_name' 'M_rs' 'M_rf' 'M_rm' 'alpha' 'me_race'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object 'Cut.off':
  'main'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    java  24.5Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object 'local_cli_theme':
  '`[environment(1)]`\cr'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) read.npc.vpc.results.Rd:16: Escaped LaTeX specials: \_
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checkRd: (-1) read.npc.vpc.results.Rd:22: Escaped LaTeX specials: \_
Documented arguments not in \usage in documentation object 'xpose.create.title':
  'plot.text' 'main'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in documentation object 'check_problem':
  'xpdb'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Invalid package aliases in Rd file 'XRjulia-package.Rd':
  'XRjulia-package'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'getCondition':
  'object'
Argument items with no description in Rd object 'screen':
  'fac' 'condition' 'position'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object 'IC':
  '\dots'
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(zebu)
  > 
  > test_check("zebu")
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 5 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_permtest.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_association_measures.R:28:3'): Mutual Information ──────────────
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_association_measures.R:28:2
   2.   └─base::namespaceImportFrom(...)
   3.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_association_measures.R:47:3'): Normalized Mutual Information ───
  Error: object 'crossprod' is not exported by 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_association_measures.R:47:2
   2.   └─base::namespaceImportFrom(...)
   3.     └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 5 ]
  Error: Test failures
  Execution halted
Malformed Description field: should contain one or more complete sentences.
Auto-generated content requiring editing in Rd object 'ZIBseq-package':
  \seealso: '~~ Optional links to other man pages, e.g. ~~ ~~ \code{\link...'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'zdat'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    NEW DEPENDENCIES
Documented arguments not in \usage in documentation object 'plot_curves':
  'fix.x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘acceldata2.RData’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package which this enhances but not available for checking: ‘asreml’
checkRd: (-1) BerryMielke.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) BlairLacy.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) Kvalseth.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) consensus.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) dsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) l.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) var.variance.Rd:12: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: ‘ggseas’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ call to ‘network’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggcorrplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘asteRiskData’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Package required but not available: ‘seasonal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘bain/libs/bain.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘Bain.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘Bain.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘fdpbandsdata’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Earlier versions
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
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: \$
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [112, 115] is out of the bounds [0, 112] of object ‘cbetaAllRow’ with type ‘arma::uvec’ {aka ‘arma::Col<unsigned int>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bayesm.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.3.0-8) 12.3.0’
'LazyData' is specified without a 'data' directory
File ‘bayesQR/libs/bayesQR.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Objects: ‘QRb_AL_mcmc.o’, ‘QRb_mcmc.o’, ‘QRc_AL_mcmc.o’,
      ‘QRc_mcmc.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Objects: ‘QRb_AL_mcmc.o’, ‘QRb_mcmc.o’, ‘QRc_AL_mcmc.o’,
      ‘QRc_mcmc.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘setseed.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘fabiabreast.txt’
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
S3 methods shown with full name in documentation object ‘export.bce’:
  ‘export.bce’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package required but not available: ‘seasonal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘BFpack/libs/BFpack.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘bct_continuous_final.o’
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘bct_prior.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘bct_continuous_final.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Objects: ‘bct_continuous_final.o’, ‘bct_prior.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘SoDA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘lavaan.survey’
Unknown package ‘lavaan.survey’ in Rd xrefs
Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
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’.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘outputs’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘select.cfs’:
  ‘select.cfs’

S3 methods shown with full name in documentation object ‘select.fast.filter’:
  ‘select.fast.filter’

S3 methods shown with full name in documentation object ‘select.forward.Corr’:
  ‘select.forward.Corr’

S3 methods shown with full name in documentation object ‘select.forward.wrapper’:
  ‘select.forward.wrapper’

S3 methods shown with full name in documentation object ‘select.inf.chi2’:
  ‘select.inf.chi2’

S3 methods shown with full name in documentation object ‘select.inf.gain’:
  ‘select.inf.gain’

S3 methods shown with full name in documentation object ‘select.inf.symm’:
  ‘select.inf.symm’

S3 methods shown with full name in documentation object ‘select.process’:
  ‘select.process’

S3 methods shown with full name in documentation object ‘select.relief’:
  ‘select.relief’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Running examples in ‘bioRad-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: select_vpfiles
> ### Title: Select vertical profile ('vp') files from computer
> ### Aliases: select_vpfiles
> 
> ### ** Examples
> 
> select_vpfiles(
+   date_min = "2016-10-03",
+   date_max = "2016-10-05",
+   radars = "bejab",
+   directory = "my_data"
+ )
Warning in open.connection(file, "rt") :
  cannot open URL 'https://lw-enram.s3-eu-west-1.amazonaws.com/radars.csv': HTTP status was '404 Not Found'
Error in open.connection(file, "rt") : 
  cannot open the connection to 'https://lw-enram.s3-eu-west-1.amazonaws.com/radars.csv'
Calls: select_vpfiles ... <Anonymous> -> read.table -> open -> open.connection
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [176, 183] is out of the bounds [0, 176] of object ‘nMaxCritMet’ with type ‘arma::rowvec’ {aka ‘arma::Row<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bmabasket.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.3.0-8) 12.3.0’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bpca.Rd:85: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object ‘xtable.bpca’:
  ‘xtable.bpca’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
S3 methods shown with full name in documentation object ‘subset.int’:
  ‘subset.int’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) brr-package.Rd:33: Escaped LaTeX specials: \&
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tmp.txt’
Found the following files/directories:
  ‘MDA231_tree.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hotcold.csv’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
'LazyData' is specified without a 'data' directory
Unexported objects imported by ‘:::’ calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘alr3’
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major refactoring of the code
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object ‘select.cglasso’:
  ‘select.cglasso’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘internals’:
  ‘max.rss’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘wallace’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘darts’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘clusterhap_reports’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tobit1’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘PopGenome’
Package suggested but not available for checking: ‘disttree’
'LazyData' is specified without a 'data' directory
checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Package suggested but not available for checking: ‘userfriendlyscience’
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unexported object imported by a ‘:::’ call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘CAM’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘paleobioDB’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) egde.Rd:26: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object ‘mChoose’:
  ‘mc.est.raw’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggcorrplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘multicolor’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘BEST’
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Non-visible changes:
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
File ‘crimCV/libs/crimCV.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘crimCV.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘crimCV.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘crimCV.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major features
    Minor features
checkRd: (-1) handmovement.Rd:9: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggcorrplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘internals’:
  ‘qr.gs’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'gurobi', 'rcbc'
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘my new data set.rds’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘seasonal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dblog’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object ‘dbglm-inl’:
  ‘dbglm.iteration’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘smd_table.docx’
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rdonlp2’
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘Rdonlp2’
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.N’ ‘.Nmiss’ ‘.Q1’ ‘.Q3’ ‘.factorN’ ‘.factorNmiss’ ‘.factorQ1’
  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
  ‘.factorsd’ ‘.max’ ‘.mean’ ‘.median’ ‘.min’ ‘.sd’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) phihat.Rd:34: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
checkRd: (-1) sammy.Rd:51: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘discreteMTP’
Unknown package ‘discreteMTP’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BOLTSSIRR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
S3 methods shown with full name in documentation object ‘add.joint.mean.many’:
  ‘all.cond.mean.PO’ ‘all.cond.mean2.PO’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
Specified C++11: please drop specification unless essential
Found the following calls to attach():
File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘OpenMPController’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
Unknown package ‘broomExtra’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [112, 115] is out of the bounds [0, 112] of object ‘i_end’ with type ‘arma::uvec’ {aka ‘arma::Col<unsigned int>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dsfa.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.3.0-8) 12.3.0’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lle’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    20181118
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘lavaan.survey’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  emd-rubner.c:810:20: warning: ‘minI’ is used uninitialized [-Wuninitialized]
  emd-rubner.c:810:26: warning: ‘minJ’ is used uninitialized [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/emdist.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.3.0-8) 12.3.0’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RStoolbox’
Found the following files/directories:
  ‘Environmental variables.csv’ ‘Inf.txt’ ‘List of species.csv’ ‘Mean
  overlap among taxa.csv’ ‘Overlap among taxa.csv’ ‘Pointsize.dat’
  ‘Polar coordinates.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Package suggested but not available for checking: ‘ggcorrplot’
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘epidict’
GNU make is a SystemRequirements.
S3 methods shown with full name in documentation object ‘addDrug.Lexis’:
  ‘addDrug.Lexis’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Rd warning: no hsearch.rds meta data for package ergm
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ergm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.3.0-8) 12.3.0’
S3 methods shown with full name in documentation object ‘summary.error_interval’:
  ‘summary.error_interval’

S3 methods shown with full name in documentation object ‘summary.measure’:
  ‘summary.measure’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘ETAS-internal’:
  ‘Smooth.catalog’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Running ‘testthat.R’ [3s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(europepmc)
  > 
  > test_check("europepmc")
  [ FAIL 1 | WARN 0 | SKIP 20 | PASS 0 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • On CRAN (20): 'test_annotations_by_id.r:4:3', 'test_epmc_citations.r:4:3',
    'test_epmc_db.r:4:3', 'test_epmc_db_count.r:4:3', 'test_epmc_details.r:4:3',
    'test_epmc_ftxt.r:4:3', 'test_epmc_ftxt_book.r:4:3', 'test_epmc_hits.r:4:3',
    'test_epmc_hits_trend.R:4:3', 'test_epmc_hits_trend.R:30:3',
    'test_epmc_lablinks.r:4:3', 'test_epmc_lablinks_count.r:4:3',
    'test_epmc_profile.r:4:3', 'test_epmc_profile.r:22:3',
    'test_epmc_refs.r:4:3', 'test_epmc_search.r:4:3', 'test_epmc_search.r:54:3',
    'test_epmc_search_by_doi.r:4:3', 'test_epmc_tm.r:4:3',
    'test_epmc_tm_count.r:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_epmc_hits_trend.R:39:3'): epmc_hits_trend synonym search works correctly ──
  <http_404/http_400/http_error/error/condition>
  Error in `rebi_GET(path = paste0(rest_path(), "/profile"), query = args)`: Not Found (HTTP 404).
  Backtrace:
      ▆
   1. └─europepmc::epmc_hits_trend("malaria", period = 2012:2016, synonym = FALSE) at test_epmc_hits_trend.R:39:2
   2.   └─base::lapply(...)
   3.     └─europepmc (local) FUN(X[[i]], ...)
   4.       └─europepmc::epmc_profile(queryforall, synonym)
   5.         └─europepmc:::rebi_GET(...)
   6.           └─httr::stop_for_status(req)
  
  [ FAIL 1 | WARN 0 | SKIP 20 | PASS 0 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘ggcorrplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘sample .nwk’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘seasonal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘ExactData’
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘iptools’ in Rd xrefs
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cec2013’
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hoa’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘exuberdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ATAforecasting’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Bogota.tex’ ‘DogBreeds1.tex’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Package suggested but not available for checking: ‘hier.part’
Unknown package ‘hier.part’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘coxKM’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) Scent.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) Traffic.Rd:44: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Found the following significant warnings:
  Rconnection.cc:282:52: warning: format ‘%p’ expects argument of type ‘void*’, but argument 3 has type ‘Rexp*’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘NNLM’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
Unexported objects imported by ‘:::’ calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
S3 methods shown with full name in documentation object ‘xtable.fdt’:
  ‘xtable.fdt’ ‘xtable.fdt.multiple’ ‘xtable.fdt_cat.multiple’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘seasonal’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘MicrobeDS’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘diveRsity’
Unknown package ‘diveRsity’ in Rd xrefs
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'nCDunnett', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) cclust.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) randIndex.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:28: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘FPCEnv’
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
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘flux.CH4.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘seasonal’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘seasonal’
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘frailtypack/libs/frailtypack.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Objects: ‘Integrale_mult_scl.o’, ‘autres_fonctions.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘autres_fonctions.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'dggrids', 'INLA'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
S3 methods shown with full name in documentation object ‘plot.funData’:
  ‘plot.funData’

S3 methods shown with full name in documentation object ‘plot.irregFunData’:
  ‘plot.irregFunData’

S3 methods shown with full name in documentation object ‘plot.multiFunData’:
  ‘plot.multiFunData’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
Specified C++14: please drop specification unless essential
‘:::’ call which should be ‘::’: ‘graphics:::grid’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ‘:::’ calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gputools’
Package suggested but not available for checking: ‘paleofire’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) plot_summary.Rd:14: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘genderdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) getopt.Rd:60: Escaped LaTeX specials: \#
Package suggested but not available for checking: ‘argon2’
Package suggested but not available for checking: ‘RGtk2’
checkRd: (-1) estGF.Rd:106: Escaped LaTeX specials: \&
checkRd: (-1) estGF.Rd:107: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggcorrplot.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
‘:::’ call which should be ‘::’: ‘scales:::censor’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ‘:::’ call: ‘productplots:::bound’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'captioner', 'lixoftConnectors'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘seasonal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggcorrplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Unknown package ‘IC2’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlr3proba’
'LazyData' is specified without a 'data' directory
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
File ‘gmeta/libs/gmeta.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘confdistint.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘confdistint.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ganalytics’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘groc.fit’:
  ‘groc.fit’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘groupsubsetselection/libs/groupsubsetselection.so’:
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘gss.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) gsym.point.Rd:143: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RRprof.out’
Packages required but not available: 'seasonal', 'x13binary'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) GUTS-package.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:201: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:209: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) luzdat.Rd:21: Escaped LaTeX specials: \~
File ‘GWEX/libs/GWEX.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘GWex_disag.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.ga.breed’ ‘.ga.fitness’ ‘.ga.init’ ‘.ga.mutate’ ‘.ga.step’
  ‘.ga.weight’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) schools.Rd:18: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘defunct’:
  ‘anova.mean’ ‘print.glht.mmc.multicomp’ ‘coef.arima.HH’ ‘glht.mmc’
  ‘plot.odds.ratio’ ‘persp.plane’ ‘persp.floor’ ‘persp.back.wall.x’
  ‘persp.back.wall.y’ ‘persp.setup’ ‘plot.hov’ ‘plot.hov.bf’
  ‘plot.matchMMC’ ‘seqplot.forecast’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘colorfulVennPlot’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Trancura9414001.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) Trancura9414001.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) hydroPSO.Rd:390: Escaped LaTeX specials: \&
checkRd: (-1) hydroPSO.Rd:408: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘AIC.txt’ ‘AICc.txt’ ‘IAS.pdf’ ‘IAS2.pdf’ ‘IAS3.pdf’
  ‘P.microlepis-AIC.txt’ ‘P.microlepis-AICc.txt’ ‘P.microlepis-IAS.pdf’
  ‘P.microlepis-IAS2.pdf’ ‘P.microlepis-IAS3.pdf’
Package suggested but not available for checking: ‘gutenbergr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SparkR’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘icd’
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
S3 methods shown with full name in documentation object ‘orlm’:
  ‘orlm.forboot.fixed’ ‘orlm.forboot’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) pulmonary.Rd:13: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object ‘internals’:
  ‘plot.page’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘IFCdata’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘seasonal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘gurobi’
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Package suggested but not available for checking: ‘cmdstanr’
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘surveyspec’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object ‘print.Item’:
  ‘print.Item’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘RMTplot.pdf’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggcorrplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘remMap’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
Dependence on R version ‘4.1.2’ not with patchlevel 0
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘bw.abram.temp’:
  ‘bw.abram.temp’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘unlist.constr’:
  ‘unlist.constr’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Killed after ’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘VARSEDIG’
Unknown package ‘VARSEDIG’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘variablekey.Rnw’ using Sweave
Error: processing vignette ‘variablekey.Rnw’ failed with diagnostics:
Running ‘texi2dvi’ on ‘variablekey.tex’ failed.
LaTeX errors:
! TeX capacity exceeded, sorry [input stack size=10000].
\protect ->\noexpand \protect 
                              \noexpand 
l.662 ... variable key\label{sec:Editing-the-key}}
                                                  
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'variablekey.Rnw'

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

Error: Vignette re-building failed.
Execution halted
S3 methods shown with full name in documentation object ‘stat.functions’:
  ‘kappa.cor’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ergm.userterms’
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package ‘ergm.userterms’ in Rd xrefs
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'akmedoids', 'clusterCrit'
Unknown packages ‘clusterCrit’, ‘akmedoids’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    lcars.0.3.1
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gpclib’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) Read.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:92: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:98: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:104: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:105: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:106: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:107: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:108: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:109: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:110: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:111: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:112: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:114: Escaped LaTeX specials: \# \#
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object ‘BIC.threshold’:
  ‘BIC.threshold’

S3 methods shown with full name in documentation object ‘BIC.threshold.ggm’:
  ‘BIC.threshold.ggm’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tTestTable.rda’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
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Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
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checkRd: (-1) lpepa.Rd:32: Escaped LaTeX specials: \&
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checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Found the following files/directories:
  ‘test’
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Package suggested but not available for checking: ‘depth’
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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No news entries found.
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Package unavailable to check Rd xrefs: ‘INLA’
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'LazyData' is specified without a 'data' directory
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Package required but not available: ‘ggcorrplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
checkRd: (-1) sw_sfac.Rd:24: Escaped LaTeX specials: \_
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checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
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S3 methods shown with full name in documentation object ‘set.scale’:
  ‘scale.dm’ ‘scale.par’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘gurobi’
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Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
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checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
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Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
'LazyData' is specified without a 'data' directory
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checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
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Found the following significant warnings:
  datablock.h:124:42: warning: pointer used after ‘void operator delete(void*)’ [-Wuse-after-free]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MCMCpack.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.3.0-8) 12.3.0’
* used C++ compiler: ‘g++-12 (Debian 12.3.0-8) 12.3.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘cmdstanr’
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
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checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘MethylCapSig’
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Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
'LazyData' is specified without a 'data' directory
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checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) dslp.Rd:11: Escaped LaTeX specials: \&
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File ‘MEtest/libs/MEtest.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘TScomp.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘TScomp.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
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checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
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Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘mvPot’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'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: ‘structSSI’
'LazyData' is specified without a 'data' directory
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No news entries found.
S3 methods shown with full name in documentation object ‘complete.miceadds’:
  ‘complete.mids.nmi’ ‘complete.mids.1chain’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘midfielddata’
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘gurobi’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
‘:::’ call which should be ‘::’: ‘parallel:::detectCores’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘l1_similarity’
checkRd: (-1) AKMCS.Rd:215: Escaped LaTeX specials: \&
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checkRd: (-1) SubsetSimulation.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) oscillator_d6.Rd:14: Escaped LaTeX specials: \&
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Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [176, 183] is out of the bounds [0, 176] of object ‘b’ with type ‘arma::vec’ {aka ‘arma::Col<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mixedClust.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.3.0-8) 12.3.0’
Specified C++11: please drop specification unless essential
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
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  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
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Package suggested but not available for checking: ‘mixRasch’
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
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No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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No news entries found.
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Flury’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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No news entries found.
Package suggested but not available for checking: ‘alstructure’

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Package suggested but not available for checking: ‘ArchR’
'LazyData' is specified without a 'data' directory
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * efourier with default norm=TRUE now messages about how wrong it may be
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
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checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
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checkRd: (-1) lines.cjs.Rd:15: Escaped LaTeX specials: \$
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘pca.plot.wrap’:
  ‘lda.plot.wrap.1’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) MultBiplotR-package.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) MultBiplotR-package.Rd:52: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggstatsplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RegularizedSCA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
‘:::’ call which should be ‘::’: ‘lhs:::maximinLHS’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_ \_
checkRd: (-1) makeNetwork.Rd:31: Escaped LaTeX specials: \_
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) nltm.control.Rd:29: Escaped LaTeX specials: \$
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Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘mail’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 41-45 [specific-dataset] (introduction.Rmd)
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
Timeout was reached: [www.nomisweb.co.uk] Resolving timed out after 10000 milliseconds
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ardechedata.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) nsRFA-package.Rd:231: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘numOSL/libs/numOSL.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘diffev.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Objects: ‘mcCAM.o’, ‘mcFMM2.o’, ‘mcFMM3.o’, ‘mcFMM4.o’, ‘mcMam3.o’,
      ‘mcMam4.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Objects: ‘mcCAM.o’, ‘mcFMM2.o’, ‘mcFMM3.o’, ‘mcFMM4.o’, ‘mcMam3.o’,
      ‘mcMam4.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘unary_ops’:
  ‘log10.ProcessNode’ ‘log10.ProcessGraphParameter’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [176, 183] is out of the bounds [0, 176] of object ‘b’ with type ‘arma::vec’ {aka ‘arma::Col<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ordinalClust.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.3.0-8) 12.3.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘pamr-internal’:
  ‘print.nsc’ ‘print.nsccv’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [176, 183] is out of the bounds [0, 176] of object ‘prior_block’ with type ‘arma::vec’ {aka ‘arma::Col<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PartialNetwork.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.3.0-8) 12.3.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggcorrplot’
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending-partition.Rmd’ using rmarkdown
--- finished re-building ‘extending-partition.Rmd’

--- re-building ‘introduction-to-partition.Rmd’ using rmarkdown

Quitting from lines 79-80 [unnamed-chunk-2] (introduction-to-partition.Rmd)
Error: processing vignette ‘introduction-to-partition.Rmd’ failed with diagnostics:
there is no package called 'ggcorrplot'
--- failed re-building ‘introduction-to-partition.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
S3 methods shown with full name in documentation object ‘vec_cast.partial_time’:
  ‘vec_cast.partial_time’

S3 methods shown with full name in documentation object ‘vec_cast.timespan’:
  ‘vec_cast.timespan’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘anomalize’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
S3 methods shown with full name in documentation object ‘ped’:
  ‘ped.markerNames’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘PythonInR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object ‘format.relation’:
  ‘format.relation’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘georob’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
Specified C++11: please drop specification unless essential
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
Specified C++11: please drop specification unless essential
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-penppml.Rmd’ using rmarkdown

Quitting from lines 140-155 [plot regularization path] (intro-to-penppml.Rmd)
Error: processing vignette ‘intro-to-penppml.Rmd’ failed with diagnostics:
object ‘last.bumpup’ not found
--- failed re-building ‘intro-to-penppml.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
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Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
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Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘qr.solve_exact’:
  ‘qr.solve_exact’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
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checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘ggsubplot’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sanitize_latex.Rd:49: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RStoolbox’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
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Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gpclib’
Unknown package ‘gpclib’ in Rd xrefs
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Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
File ‘popsom/libs/popsom.so’:
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘vsom.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘vsom.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tradelist-class.Rd:91: Escaped LaTeX specials: \$
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:144: Escaped LaTeX specials: \&
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checkRd: (-1) cra2.Rd:231: Escaped LaTeX specials: \&
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checkRd: (-1) cra2.Rd:237: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:301: Escaped LaTeX specials: \&
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checkRd: (-1) cra3.Rd:307: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:309: Escaped LaTeX specials: \&
checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
Unknown package ‘advclust’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘ffbase’
Unknown package ‘ffbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'gurobi', 'rcbc'
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘ProFit’
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in ‘promor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: heatmap_na
> ### Title: Visualize missing data
> ### Aliases: heatmap_na
> 
> ### ** Examples
> 
> ## Generate a raw_df object with default settings. No technical replicates.
> raw_df <- create_df(
+   prot_groups = "https://raw.githubusercontent.com/caranathunge/promor_example_data/main/pg1.txt",
+   exp_design = "https://raw.githubusercontent.com/caranathunge/promor_example_data/main/ed1.txt"
+ )
Warning in file(file, "rt") :
  URL 'https://raw.githubusercontent.com/caranathunge/promor_example_data/main/pg1.txt': Timeout of 60 seconds was reached
Error in file(file, "rt") : 
  cannot open the connection to 'https://raw.githubusercontent.com/caranathunge/promor_example_data/main/pg1.txt'
Calls: create_df -> read.csv -> read.table -> file
Execution halted
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cin’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) Ch0C-plot.cpd.PwrGSD.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggcorrplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘internals’:
  ‘format.perc’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘spDataLarge’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object ‘internals’:
  ‘plot.piqr2’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘predict.iqrL.internal’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘fastshp’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) qwraps2.Rd:73: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘googlesheets’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘export.default’:
  ‘export.default’

S3 methods shown with full name in documentation object ‘export.listpoly’:
  ‘export.listpoly’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘rcanvec.cache’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘data.csv’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘outcmaesdisp.dat’
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
S3 methods shown with full name in documentation object ‘editDataset.design’:
  ‘editDataset.design’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package suggested but not available for checking: ‘conics’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘devAll’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DIDmultiplegt’
Specified C++11: please drop specification unless essential
checkRd: (-1) re2_syntax.Rd:539: Escaped LaTeX specials: \_
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) calc.relimp.Rd:41: Escaped LaTeX specials: \~
checkRd: (-1) classesmethods.relaimpo.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) classesmethods.relaimpo.Rd:104: Escaped LaTeX specials: \$
checkRd: (-1) mianalyze.relimp.Rd:69: Escaped LaTeX specials: \~
checkRd: (-1) mianalyze.relimp.Rd:73: Escaped LaTeX specials: \~
checkRd: (-1) relimplm-class.Rd:63: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbootMI-class.Rd:121: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbooteval-class.Rd:146: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:42: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘reReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.reReg
> ### Title: Plot the Baseline Cumulative Rate Function and the Baseline
> ###   Cumulative Hazard Function
> ### Aliases: plot.reReg
> ### Keywords: Plots
> 
> ### ** Examples
> 
> data(simDat)
> fm <- Recur(t.start %to% t.stop, id, event, status) ~ x1 + x2
> 
> fit <- reReg(fm, data = simDat, B = 0)
> plot(fit)
> plot(fit, xlab = "Time (days)", smooth = TRUE)
> 
> ## Predicted cumulative rate and hazard given covariates
> newdata <- expand.grid(x1 = 0:1, x2 = mean(simDat$x2))
> plot(fit, newdata = newdata, showName = TRUE)
Error in get(method[[1]]) : object 'last.bumpup' not found
Calls: <Anonymous> ... drawDetails -> drawDetails.dlgrob -> apply.method -> get
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CardioRiskFactors.Rd:35: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) columbus.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) columbus.Rd:30: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
'LazyData' is specified without a 'data' directory
Non-standard file/directory found at top level:
  ‘jri’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object ‘fitted.values.margint’:
  ‘fitted.values.margint’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rnaturalearthhires’
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  /usr/lib/gcc/x86_64-linux-gnu/12/include/emmintrin.h:134:24: warning: array subscript ‘__m128d_u[0]’ is partly outside array bounds of ‘Eigen::internal::plain_matrix_type<Eigen::Product<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>, Eigen::Transpose<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false> >, 0>, Eigen::Dense>::type [1]’ {aka ‘Eigen::Matrix<double, 1, 1, 0, 1, 1> [1]’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RobustGaSP.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.3.0-8) 12.3.0’
* used C++ compiler: ‘g++-12 (Debian 12.3.0-8) 12.3.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  vendor/boost/intrusive/detail/slist_node.hpp:56:16: warning: pointer used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free]
  vendor/boost/intrusive/detail/hook_traits.hpp:77:10: warning: pointer used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RPostgres.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.3.0-8) 12.3.0’
* used C++ compiler: ‘g++-12 (Debian 12.3.0-8) 12.3.0’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘Tsttwalk.dat’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object ‘printHTML.trackInfo’:
  ‘printHTML.trackInfo’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘results’
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘glmmADMB’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
S3 methods shown with full name in documentation object ‘matmult’:
  ‘%*%.rv’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) mapBubbles.Rd:62: Escaped LaTeX specials: \$
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘networkTomography’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘santoku-cast’:
  ‘santoku_cast_common.default’ ‘santoku_cast_common.double’
  ‘santoku_cast_common.Date’ ‘santoku_cast_common.POSIXct’
  ‘santoku_cast_common.ts’ ‘santoku_cast_common.zoo’
  ‘santoku_cast_common.integer64’ ‘santoku_cast_common.hexmode’
  ‘santoku_cast_common.octmode’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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: ‘FitARMA’
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
‘library’ or ‘require’ call to ‘progress’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘ssvd’
Unexported object imported by a ‘:::’ call: ‘simplifyEnrichment:::is_GO_id’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘plot’:
  ‘plot.discretization’

S3 methods shown with full name in documentation object ‘predict’:
  ‘predict.discretization’ ‘predict.reject_infered’

S3 methods shown with full name in documentation object ‘summary’:
  ‘summary.discretization’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘untitled_consensus_cluster’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘ggcorrplot’
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘x13binary’

Package suggested but not available for checking: ‘seasonalview’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spgrass6’
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘min.abs’:
  ‘min.abs’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fahst.rd:39: Escaped LaTeX specials: \^
checkRd: (-1) fahst.rd:36: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:46: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:42: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:43: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:49: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:44: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:46: Escaped LaTeX specials: \^
checkRd: (-1) hsortplot.rd:24: Escaped LaTeX specials: \^
checkRd: (-1) nappesortplot.Rd:30: Escaped LaTeX specials: \^
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checkRd: (-1) plot.fahst.rd:45: Escaped LaTeX specials: \^
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checkRd: (-1) print.fast.Rd:22: Escaped LaTeX specials: \^
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GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘sequoia/libs/sequoia.so’:
  Found ‘_gfortran_arandom_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘SimGenoErrors.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘SimGenoErrors.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 44-48 [unnamed-chunk-3] (introduction.Rmd)
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `loadNamespace()`:
! there is no package called 'prettymapr'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) gPLS.Rd:72: Escaped LaTeX specials: \^
checkRd: (-1) gPLS.Rd:74: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:67: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:69: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:75: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:77: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ggcorrplot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘ExportFigtree1.tre’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘SimRAD-exampleRefSeq-Fasta.fa’ ‘SimRAD-exampleRefSeq.fa’
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘fg_step_tab_pp’
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ‘:::’ call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘texPreview’
Unknown package ‘texPreview’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘captioner’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Unknown package ‘InformationValue’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘SmoothHazard/libs/SmoothHazard.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘bgos.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘my_new_social_media_plot.png’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘.R_Test’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.solveEnv’
S3 methods shown with full name in documentation object ‘plot.predictions’:
  ‘plot.predictions’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘r2cytoscape’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
Package suggested but not available for checking: ‘NLMR’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Unknown package ‘sparsebn’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat.data', 'spatstat',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'

Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package unavailable to check Rd xrefs: ‘RandomFields’
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'
Package unavailable to check Rd xrefs: ‘RandomFields’
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spDataLarge’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.neig’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
Specified C++11: please drop specification unless essential
checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggcorrplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
Package suggested but not available for checking: ‘starsdata’
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘imputeMissings’
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘corrviz.html’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myNewStrat.R’
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RFOC’
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
Package suggested but not available for checking: ‘seasonal’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘size.penalize’:
  ‘size.penalize’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘extraTrees’
Unknown package ‘extraTrees’ in Rd xrefs
Package suggested but not available for checking: ‘extraTrees’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
surfaceSimulate : phytransform: no visible global function definition
  for ‘rescale’
Undefined global functions or variables:
  rescale
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'INLA', 'gpclib'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
Specified C++11: please drop specification unless essential
Unknown package ‘survJamda’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) diabetes.Rd:18: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘swdpwr/libs/swdpwr.so’:
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘auxillary.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘auxillary.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘swephRdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.csv’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘designMatrices’:
  ‘print.designMatrices’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘R2wd’
checkRd: (-1) R2txt.Rd:164: Escaped LaTeX specials: \#
checkRd: (-1) bct.Rd:18: Escaped LaTeX specials: \^
checkRd: (-1) bct.Rd:19: Escaped LaTeX specials: \^
checkRd: (-1) ineq.Rd:10: Escaped LaTeX specials: \&
checkRd: (-1) put.points.demo.Rd:39: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:10: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:31: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Rd file 'textEmbedReduce.Rd':
  \usage lines wider than 90 characters:
         "https://raw.githubusercontent.com/adithya8/ContextualEmbeddingDR/master/models/fb20/scalar.csv",
         "https://raw.githubusercontent.com/adithya8/ContextualEmbeddingDR/master/models/fb20/rpca_roberta_768_D_20.csv"

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Unknown package ‘textreadr’ in Rd xrefs
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/memory.hpp:127:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/textTinyR.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.3.0-8) 12.3.0’
* used C++ compiler: ‘g++-12 (Debian 12.3.0-8) 12.3.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
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checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggcorrplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  common.c:36:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/tiff.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.3.0-8) 12.3.0’
Specified C++11: please drop specification unless essential
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package required but not available: ‘ggcorrplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'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: ‘moveVis’
Unknown package ‘moveVis’ in Rd xrefs
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR'
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘TreeDistData’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug fixes
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
Package suggested but not available for checking: ‘seasonal’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [100s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tsbox)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("tsbox")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 650 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • On CRAN (17): 'test-error_handling.R:237:3',
    'test-nonstandard_cnames.R:20:3', 'test-nonstandard_cnames.R:58:3',
    'test-readme.R:2:3', 'test-object_conversion.R:6:3',
    'test-object_conversion.R:47:3', 'test-object_conversion.R:83:3',
    'test-object_conversion.R:114:3', 'test-object_conversion.R:151:3',
    'test-ts_.R:19:3', 'test-ts_first_of_period.R:1:1',
    'test-ts_frequency.R:28:3', 'test-ts_index.R:2:1', 'test-ts_plot.R:2:3',
    'test-ts_summary.R:7:3', 'test-tsibble.R:44:3', 'test-tzone.R:8:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-units.R:40:5'): tsbox works with units ─────────────────────────
  Error: Additional packages needed. To install, use:
  
    install.packages("seasonal")
  Backtrace:
      ▆
   1. └─fl[[i]](x) at test-units.R:40:4
   2.   └─tsbox::load_suggested("seasonal")
   3.     └─tsbox:::stop0(...)
  
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 650 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘tseriesTARMA/libs/tseriesTARMA.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘TARMA_MOD.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘tsibble-vctrs’:
  ‘vec_ptype2.tbl_ts’ ‘vec_cast.tbl_ts’ ‘vec_cast.yearmonth’
  ‘vec_ptype2.yearmonth’ ‘vec_cast.yearquarter’
  ‘vec_ptype2.yearquarter’ ‘vec_cast.yearweek’ ‘vec_ptype2.yearweek’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) lindner.Rd:44: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘ggstatsplot’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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: ‘USA.state.boundaries.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘syntab’:
  ‘print.syntab’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
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checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) checkTS.VGAMextra.Rd:176: Escaped LaTeX specials: \&
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    NEW FEATURES
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘prepr’
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘QIC.gee’:
  ‘QIC.gee’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Package suggested but not available for checking: ‘anomalize’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘x13binary’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
File ‘xbreed/libs/xbreed.so’:
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘hp.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘hp.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) read.npc.vpc.results.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) read.npc.vpc.results.Rd:19: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) read.npc.vpc.results.Rd:22: Escaped LaTeX specials: \_
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Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘zdat’
Problems with news in ‘NEWS.md’:
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    NEW DEPENDENCIES
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
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checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘acceldata2.RData’
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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Package suggested but not available for checking: ‘INLA’
Package which this enhances but not available for checking: ‘asreml’
checkRd: (-1) BerryMielke.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) BlairLacy.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) Kvalseth.Rd:11: Escaped LaTeX specials: \&
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checkRd: (-1) var.variance.Rd:12: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
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checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
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checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ call to ‘network’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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’.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘asteRiskData’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘fdpbandsdata’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Earlier versions
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
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: \$
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayesdfa.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayesGAM.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [112, 115] is out of the bounds [0, 112] of object ‘cbetaAllRow’ with type ‘arma::uvec’ {aka ‘arma::Col<unsigned int>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayesm.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.3.0-8) 12.3.0’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘blavaan’
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘fabiabreast.txt’
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
S3 methods shown with full name in documentation object ‘export.bce’:
  ‘export.bce’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SoDA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘lavaan.survey’
Unknown package ‘lavaan.survey’ in Rd xrefs
Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
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’.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘outputs’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘select.cfs’:
  ‘select.cfs’

S3 methods shown with full name in documentation object ‘select.fast.filter’:
  ‘select.fast.filter’

S3 methods shown with full name in documentation object ‘select.forward.Corr’:
  ‘select.forward.Corr’

S3 methods shown with full name in documentation object ‘select.forward.wrapper’:
  ‘select.forward.wrapper’

S3 methods shown with full name in documentation object ‘select.inf.chi2’:
  ‘select.inf.chi2’

S3 methods shown with full name in documentation object ‘select.inf.gain’:
  ‘select.inf.gain’

S3 methods shown with full name in documentation object ‘select.inf.symm’:
  ‘select.inf.symm’

S3 methods shown with full name in documentation object ‘select.process’:
  ‘select.process’

S3 methods shown with full name in documentation object ‘select.relief’:
  ‘select.relief’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Running examples in ‘bioRad-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: select_vpfiles
> ### Title: Select vertical profile ('vp') files from computer
> ### Aliases: select_vpfiles
> 
> ### ** Examples
> 
> select_vpfiles(
+   date_min = "2016-10-03",
+   date_max = "2016-10-05",
+   radars = "bejab",
+   directory = "my_data"
+ )
Warning in open.connection(file, "rt") :
  cannot open URL 'https://lw-enram.s3-eu-west-1.amazonaws.com/radars.csv': HTTP status was '404 Not Found'
Error in open.connection(file, "rt") : 
  cannot open the connection to 'https://lw-enram.s3-eu-west-1.amazonaws.com/radars.csv'
Calls: select_vpfiles ... <Anonymous> -> read.table -> open -> open.connection
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/blavaan.Rcheck/00install.out’ for details.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [176, 183] is out of the bounds [0, 176] of object ‘nMaxCritMet’ with type ‘arma::rowvec’ {aka ‘arma::Row<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bmabasket.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.3.0-8) 12.3.0’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.