'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'moveEZ.Rmd' using rmarkdown
File anim1.gif not found in resource path
Error: processing vignette 'moveEZ.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'moveEZ.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.3Mb
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    doc       4.8Mb
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    libs      1.0Mb
checkRd: (-1) glmfence.Rd:21: Lost braces; missing escapes or markup?
    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
checkRd: (-1) lmfence.Rd:21: Lost braces; missing escapes or markup?
    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
checkRd: (-1) get.mpt.fia.Rd:60: Lost braces
    60 | \item{lnconst}{When inequality constraints are present, \code{lnconst} serves as an adjustment of code{lnInt}. It estimates the logarithm of the proportion of parameter space [0,1]^S that satisfies those inequality constraints, and the log integral term is given by \code{lnInt+lnconst}.
       |                                                                                                       ^
checkRd: (-1) prediction.plot.Rd:38: Lost braces
    38 | The labels on the x-axis. Default is \code{Tree 1} to code{Tree n}.
       |                                                           ^
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
checkRd: (-1) MultiManhattan.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item{LogTimes}{Magnification of {-log10(P-value)}; the default is
       |                                          ^
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    35 |     \item{LODTimes}{Magnification of {LOD score}; the default is 1.2.}
       |                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) n.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    libs   1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   4.5Mb
    libs   1.2Mb
installed size is  5.2Mb
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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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checkRd: (-1) multivar_joint_shannon_entropy.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
checkRd: (-1) total_correlation.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
'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 'mtrank.Rmd' using rmarkdown
! Package pdftex.def Error: File `10b841dc41b13016bf182dbf9d29437122fd8049.pdf'
 not found: using draft setting.

Error: processing vignette 'mtrank.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/mtrank.Rcheck/vign_test/mtrank/vignettes/mtrank.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See mtrank.log for more info.
--- failed re-building 'mtrank.Rmd'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) coef.mdf.Rd:17: Lost braces; missing escapes or markup?
    17 |   \item{type}{: Argument that controls the type of parameters to be returned. If \code{type="persons"} (default), a vector with the person parameters is returned. When \code{type="items"} then a vector with the item ranks obtained by the MUDFOLD item selection algorithm is returned. If {type="all"} then a list with both person and item coefficients is returned to the user.
       |                                                                                                                                                                                                                                                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
checkRd: (-1) MultEq-package.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:30: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'SIR-MCMC.Rmd' using rmarkdown
! Package pdftex.def Error: File `c9e4a426e91498fb30e071b8b92bb987fe93d870.pdf'
 not found: using draft setting.

Error: processing vignette 'SIR-MCMC.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/MultiBD.Rcheck/vign_test/MultiBD/vignettes/SIR-MCMC.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SIR-MCMC.log for more info.
--- failed re-building 'SIR-MCMC.Rmd'

--- re-building 'SIRtrans.Rnw' using knitr
--- finished re-building 'SIRtrans.Rnw'

SUMMARY: processing the following file failed:
  'SIR-MCMC.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) dbivCMP.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{bivprob}{Bivariate probabilities, {p00, p01, p10, p11}.}
       |                                         ^
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
File ./man/figures/plot_peje.png not found in resource path
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'Introduction.Rmd'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.0Mb
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    data   1.0Mb
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'LazyData' is specified without a 'data' directory
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    4.5Mb
    libs  12.4Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
GNU make is a SystemRequirements.
checkRd: (-1) nullestimation.Rd:17: Lost braces; missing escapes or markup?
    17 |           \code{U}        \tab The common latent space vectors. U in R^{n x d}\cr
       |                                                                        ^
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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    help   2.3Mb
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'LazyData' is specified without a 'data' directory
checkRd: (-1) biomasse.Rd:30: Lost braces
    30 | Makowski, D., Jeuffroy, M.-H., Gu\'{e}rif, M., 2004 Bayesian methods for
       |                                    ^
checkRd: (-1) climat.Rd:20: Lost braces
    20 | Makowski, D., Jeuffroy, M.-H., Gu\'{e}rif, M., 2004 Bayesian methods for
       |                                    ^
checkRd: (-1) simulmodel.Rd:15: Lost braces
    15 |   \item{\dots}{... }{possible fixed parameters of the R-function}
       |                     ^
installed size is  5.1Mb
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Error(s) in re-building vignettes:
--- re-building 'multiview.Rmd' using rmarkdown
! Package pdftex.def Error: File `4966fce381610d612d30b1096abb82f2ac1edaff.pdf'
 not found: using draft setting.

Error: processing vignette 'multiview.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/multiview.Rcheck/vign_test/multiview/vignettes/multiview.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See multiview.log for more info.
--- failed re-building 'multiview.Rmd'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
checkRd: (-1) metricUnfolding.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:73-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:75-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:80-86: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
install log '' does not exist
Package suggested but not available for checking: 'cmdstanr'
installed size is 11.1Mb
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    R     7.4Mb
    doc   2.0Mb
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
checkRd: (-1) MVNtestchar-package.Rd:16-17: Lost braces; missing escapes or markup?
    16 | {Provides a test of multivariate normality of a sample which does not require estimation of the nuisance parameters, the mean      vector and covariance matrix.  Rather, a sequence of transformations removes these nuisance parameters, resulting in a set of    sample matrices that are positive definite.  If, and only if the original data is multivariate normal, these matrices are       uniformly distributed on the space of positive definite matrices in the unit hyper-rectangle.  The package performs a goodness    of fit test of this hypothesis. In addition to the test, functions in the package give visualizations of the  support region    of positive definite matrices for p equals 2.
       | ^
'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: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rTubeDB'
Package unavailable to check Rd xrefs: 'rTubeDB'
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'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
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    doc    6.1Mb
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checkRd: (-1) mzipmed_data.Rd:22: Lost braces; missing escapes or markup?
    22 | @source {Simulated to serve as an example}
       |         ^
Package which this enhances but not available for checking: 'asreml'
installed size is 16.2Mb
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checkRd: (-1) M36NT2PM.dat.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) M36NT2PM.dat.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) DSIVdata.Rd:15-23: Lost braces
    15 | for(i in 1:50){
       |               ^
checkRd: (-1) DSIVdata.Rd:17-21: Lost braces
    17 |   for(j in 1:50){
       |                 ^
checkRd: (-1) DSIVdata.Rd:31-39: Lost braces
    31 | for(i in 1:20){
       |               ^
checkRd: (-1) DSIVdata.Rd:33-37: Lost braces
    33 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:10-18: Lost braces
    10 | for(i in 1:200){
       |                ^
checkRd: (-1) DSLIVEdata.Rd:12-16: Lost braces
    12 |   for(j in 1:200){
       |                  ^
checkRd: (-1) DSLIVEdata.Rd:26-34: Lost braces
    26 | for(i in 1:20){
       |               ^
checkRd: (-1) DSLIVEdata.Rd:28-32: Lost braces
    28 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:50-54: Lost braces
    50 | for(kk in 1:length(p)){
       |                       ^
checkRd: (-1) drop_name_crossref.Rd:49: Lost braces; missing escapes or markup?
    49 | Takes one or several dois and extracts information from Crossref, then processes them into visual citations with \code{\link{drop_name}}. Requires {rcrossref} > v1.1, see README for further details.
       |                                                                                                                                                    ^
installed size is  5.5Mb
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    libs     2.4Mb
    models   1.1Mb
checkRd: (-1) fod.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fod.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fod.Rd:14: Lost braces in \itemize; meant \describe ?
'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  6.9Mb
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    doc    3.5Mb
installed size is  9.6Mb
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    doc    6.5Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                 ^
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                         ^
checkRd: (-1) nbconvert.Rd:49: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) nbconvert.Rd:50: Lost braces in \enumerate; meant \describe ?
Package suggested but not available for checking: 'NBDCtoolsData'
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'utils'
A package should be listed in only one of these fields.
'LazyData' is specified without 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
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    data   9.4Mb
installed size is 16.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
installed size is  8.0Mb
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    data   7.1Mb
'LazyData' is specified without a 'data' directory
Package required but not available: 'MBESS'

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
installed size is  6.5Mb
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    doc    2.4Mb
    help   1.3Mb
    libs   1.5Mb
Error(s) in re-building vignettes:
--- re-building 'netseer.Rmd' using rmarkdown
File man/figures/logo.png not found in resource path
Error: processing vignette 'netseer.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'netseer.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
checkRd: (-1) spec_clust.Rd:33: Lost braces; missing escapes or markup?
    33 | A label vector of size n x 1 with elements in {1,2,...,K}
       |                                               ^
checkRd: (-1) rc.plot.ideogram.Rd:20: Lost braces; missing escapes or markup?
    20 |  \item{las}{numeric in {0,1,2,3}; the style of chromosome labels. 0, always parallel to the track [default]; 1, always horizontal; 2, always perpendicular to the track; 3, always vertical.}
       |                        ^
Error(s) in re-building vignettes:
--- re-building 'basics.Rmd' using rmarkdown
! Package pdftex.def Error: File `f98df68f16828f271dbfe8fdb756b47f718509a0.pdf'
 not found: using draft setting.

Error: processing vignette 'basics.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/NetworkDistance.Rcheck/vign_test/NetworkDistance/vignettes/basics.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See basics.log for more info.
--- failed re-building 'basics.Rmd'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
S3 methods shown with full name in Rd file 'network.extensions.Rd':
  'get.edgeIDs.active' 'get.edges.active' 'get.neighborhood.active'
  'is.adjacent.active'

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 14.8Mb
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    libs  13.5Mb
GNU make is a SystemRequirements.
checkRd: (-1) networktree.Rd:56: Lost braces; missing escapes or markup?
    56 | with a matrix response {y}. \code{x1} and \code{x2} are used as
       |                        ^
installed size is  7.9Mb
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installed size is  6.5Mb
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    R         1.6Mb
    doc       1.1Mb
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    libs      1.4Mb
Packages suggested but not available for checking:
  'BPST', 'ImageSCC', 'Triangulation'
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'NGCHMDemoData', 'NGCHMSupportFiles'
'LazyData' is specified without a 'data' directory
checkRd: (-1) NHANES.Rd:278: Lost braces
   278 | \code{AgeFirstMarij}{Age participant first tried marijuana. Reported for participants aged 18 to 59 years.}
       |                     ^
The following files should probably not be installed:
  'nhm-manual.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
checkRd: (-1) bootstrap_param_est.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:25: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) impute.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_data.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
installed size is 27.6Mb
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installed size is  6.9Mb
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    doc       4.0Mb
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installed size is  5.7Mb
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Package which this enhances but not available for checking: 'jpndistrict'
Malformed Description field: should contain one or more complete sentences.
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
checkRd: (-1) anova.Rd:19: Lost braces
    19 |   Returns an object of class code{anova}.  These objects represent
       |                                  ^
Error(s) in re-building vignettes:
--- re-building 'FixedParameters.Rmd' using rmarkdown
--- finished re-building 'FixedParameters.Rmd'

--- re-building 'Intro-to-nlsr.Rmd' using rmarkdown
! Package pdftex.def Error: File `fbf91f55cafdb64fbb1f21a7f07983599fd4dadd.pdf'
 not found: using draft setting.

Error: processing vignette 'Intro-to-nlsr.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/nlsr.Rcheck/vign_test/nlsr/vignettes/Intro-to-nlsr.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Intro-to-nlsr.log for more info.
--- failed re-building 'Intro-to-nlsr.Rmd'

--- re-building 'R-analytic-derivatives.Rmd' using rmarkdown
Loading required package: Ryacas

Attaching package: 'Ryacas'

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

    integrate

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

    %*%, det, diag, diag<-, lower.tri, upper.tri

--- finished re-building 'R-analytic-derivatives.Rmd'

--- re-building 'nlsr-derivs.Rmd' using rmarkdown
Loading required package: Ryacas

Attaching package: 'Ryacas'

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

    integrate

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

    %*%, det, diag, diag<-, lower.tri, upper.tri

--- finished re-building 'nlsr-derivs.Rmd'

--- re-building 'nlsr-devdoc.Rmd' using rmarkdown
--- finished re-building 'nlsr-devdoc.Rmd'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'simpar'
':::' call which should be '::': 'NMdata:::dcastSe'
  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
GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
checkRd: (-1) simulatePop.Rd:40: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) simulatePop.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imp_int_an.Rd:24: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) plot.ndmodel.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:18: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
    mods   3.3Mb
Package suggested but not available for checking: 'OpenMx'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'npcs-demo.Rmd' using rmarkdown
! Package pdftex.def Error: File `a823f735f7bab93eb94e4a819fc6cea66de84c9d.pdf'
 not found: using draft setting.

Error: processing vignette 'npcs-demo.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/npcs.Rcheck/vign_test/npcs/vignettes/npcs-demo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See npcs-demo.log for more info.
--- failed re-building 'npcs-demo.Rmd'

SUMMARY: processing the following file failed:
  'npcs-demo.Rmd'

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) DiscHazRateAuxFunctions.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:48: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'NSR-Ex.R' failed
The error most likely occurred in:

> ### Name: NSR_metadata
> ### Title: Get NSR metadata
> ### Aliases: NSR_metadata
> 
> ### ** Examples
> 
> {
+ metadata <- NSR_metadata()
+ }
There appears to be a problem reaching the API.
There appears to be a problem reaching the API.
There appears to be a problem reaching the API.
Error in names(output) <- c("citations", "version", "sources") : 
  'names' attribute [3] must be the same length as the vector [0]
Calls: NSR_metadata
Execution halted
Error(s) in re-building vignettes:
--- re-building 'NSR.Rmd' using rmarkdown

Quitting from NSR.Rmd:68-79 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `names(output) <- c("citations", "version", "sources")`:
! 'names' attribute [3] must be the same length as the vector [0]
---
Backtrace:
    ▆
 1. └─NSR::NSR_metadata()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'NSR.Rmd' failed with diagnostics:
'names' attribute [3] must be the same length as the vector [0]
--- failed re-building 'NSR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) MSM.fit.Rd:21: Lost braces
    21 | \code{MSM.fit} returns an object of class code{MSM.lm} or \code{MSM.glm}, depending on the input model.
       |                                               ^
checkRd: (-1) SMC.Smooth.Rd:25: Lost braces; missing escapes or markup?
    25 | observation at current time step. It should return {xx} (the samples xt) and
       |                                                    ^
checkRd: (-1) SMC.Smooth.Rd:26: Lost braces; missing escapes or markup?
    26 | {logww} (their corresponding log weight).}
       | ^
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
  'Cubist', 'Metrics', 'arm', 'brnn', 'broom', 'car', 'caret',
  'corrplot', 'doParallel', 'dplyr', 'e1071', 'earth', 'gam', 'gbm',
  'ggplot2', 'glmnet', 'gridExtra', 'htmltools', 'htmlwidgets',
  'ipred', 'leaps', 'nnet', 'olsrr', 'parallel', 'pls', 'purrr',
  'randomForest', 'reactable', 'readr', 'rpart', 'scales', 'tidyr',
  'tree', 'vip', 'xgboost'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.4Mb
checkRd: (-1) OBMb.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                               ^
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                                         ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |        ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |                  ^
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.3Mb
    libs   1.4Mb
checkRd: (-1) onlineCPD.Rd:35: Lost braces
    35 |  function(x, lambda){const_hazard(x, lambda=100)}
       |                     ^
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ODT.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
GNU make is a SystemRequirements.
checkRd: (-1) oncotree.fit.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
'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 'geospatial-queries.Rmd' using rmarkdown
File figure/bbox-example-plot-1.png not found in resource path
Error: processing vignette 'geospatial-queries.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geospatial-queries.Rmd'

--- re-building 'ggplot2.Rmd' using rmarkdown
File figure/ggplot2-box-plot-1.png not found in resource path
Error: processing vignette 'ggplot2.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'ggplot2.Rmd'

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

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

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

--- re-building 'querying-rollups.Rmd' using rmarkdown
File figure/who-daily-avg-plot-1.png not found in resource path
Error: processing vignette 'querying-rollups.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'querying-rollups.Rmd'

SUMMARY: processing the following files failed:
  'geospatial-queries.Rmd' 'ggplot2.Rmd' 'plotting.Rmd'
  'querying-measurements.Rmd' 'querying-rollups.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'unix'
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'openCR-vignette.Rmd' using rmarkdown
! Package pdftex.def Error: File `1925a3744f487152d220f1e2e3f45d8c7d9acf5f.pdf'
 not found: using draft setting.

Error: processing vignette 'openCR-vignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/openCR.Rcheck/vign_test/openCR/vignettes/openCR-vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See openCR-vignette.log for more info.
--- failed re-building 'openCR-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs   19.9Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ifaTools'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/OpenMx.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Package suggested but not available for checking: 'openNLPmodels.en'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Package suggested but not available for checking: 'gradethis'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   1.8Mb
checkRd: (-1) MonteCarlo.Rd:23: Lost braces
    23 | N is computed from \code{p} length. M is code{10^4} by default.
       |                                              ^
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Error(s) in re-building vignettes:
--- re-building 'ASPRE_example.Rmd' using rmarkdown
! Package pdftex.def Error: File `0eaf7c8e427710ea5e018c6c3030463ec06581b1.pdf'
 not found: using draft setting.

Error: processing vignette 'ASPRE_example.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/OptHoldoutSize.Rcheck/vign_test/OptHoldoutSize/vignettes/ASPRE_example.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See ASPRE_example.log for more info.
--- failed re-building 'ASPRE_example.Rmd'

--- re-building 'comparison_of_algorithms.Rmd' using rmarkdown
! Package pdftex.def Error: File `16f519e842a28e20f48a48c2185344d4a39badd1.pdf'
 not found: using draft setting.

Error: processing vignette 'comparison_of_algorithms.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/OptHoldoutSize.Rcheck/vign_test/OptHoldoutSize/vignettes/comparison_of_algorithms.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See comparison_of_algorithms.log for more info.
--- failed re-building 'comparison_of_algorithms.Rmd'

--- re-building 'simulated_example.Rmd' using rmarkdown
! Package pdftex.def Error: File `830ece5e942c2ee018385ee2a2256185d333796b.pdf'
 not found: using draft setting.

Error: processing vignette 'simulated_example.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/OptHoldoutSize.Rcheck/vign_test/OptHoldoutSize/vignettes/simulated_example.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See simulated_example.log for more info.
--- failed re-building 'simulated_example.Rmd'

SUMMARY: processing the following files failed:
  'ASPRE_example.Rmd' 'comparison_of_algorithms.Rmd'
  'simulated_example.Rmd'

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) drawdesign.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:44: Lost braces in \itemize; meant \describe ?
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'opusreader2_introduction.Rmd' using rmarkdown
File ../images/opus-measurement-settings.png not found in resource path
Error: processing vignette 'opusreader2_introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'opusreader2_introduction.Rmd'

SUMMARY: processing the following file failed:
  'opusreader2_introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
    doc    1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) internal.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) orf.Rd:74: Lost braces
    74 | matrix of covariates \code{X} and a vector of outcomes 'code{Y} to the \code{orf}
       |                                                             ^
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
checkRd: (-1) hillEquation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:91-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) polynomial.derivatives.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:21: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) oscar.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{print}{Level of verbosity in Fortran (may not be visible on all terminals); should be an integer between {range, range}, Default: 3}
       |                                                                                                                ^
checkRd: (-1) oscar.control.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{start}{Starting point generation method, see vignettes for details; should be an integer between {range,range}, Default: 2}
       |                                                                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'groupcompare'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../osqp_sources/include/public/osqp_api_functions.h:155:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  ../osqp_sources/include/public/osqp_api_functions.h:182:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  ../osqp_sources/include/private/timing.h:21:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  ../osqp_sources/src/osqp_api.c:180:15: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  ../osqp_sources/src/osqp_api.c:196:21: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  ../osqp_sources/src/timing_windows.c:22:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/osqp.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 13.3.0'
GNU make is a SystemRequirements.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'Rcplex'
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                ^
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                                ^
checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) fmat.Rd:15: Lost braces; missing escapes or markup?
    15 | \item outcome: codes {I, P, R, NC, O, UH, UO, eUH, eUO, NE}
       |                      ^
checkRd: (-1) fmat.Rd:24: Lost braces; missing escapes or markup?
    24 | The input parameters given by the user are {I, P, R, NC, O, UH, UO} and
       |                                            ^
checkRd: (-1) fmat.Rd:25: Lost braces; missing escapes or markup?
    25 | the parameter 'e'. The parameter e is multiplied by {UH, UO} internally so as to
       |                                                     ^
checkRd: (-1) fmat.Rd:26: Lost braces; missing escapes or markup?
    26 | produce {eUH, eUO}.
       |         ^
checkRd: (-1) middleearth.Rd:14: Lost braces; missing escapes or markup?
    14 | \item \strong{code:} one of the outcome codes {I, P, R, NC, O, UH, UO, UH, UO, NE}
       |                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) MICS2014Ch.Rd:296: Lost braces in \enumerate; meant \describe ?
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checkRd: (-1) MICS2014Wm.Rd:337: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:88: Lost braces in \enumerate; meant \describe ?
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installed size is 17.9Mb
  sub-directories of 1Mb or more:
    library  17.0Mb
Package suggested but not available for checking: 'CorShrink'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'panelmatch-overview.Rmd' using rmarkdown
! Package pdftex.def Error: File `ded2b699f23c61eb9aa45a0439edc78b22a403a3.pdf'
 not found: using draft setting.

Error: processing vignette 'panelmatch-overview.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/PanelMatch.Rcheck/vign_test/PanelMatch/vignettes/panelmatch-overview.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See panelmatch-overview.log for more info.
--- failed re-building 'panelmatch-overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) hvidovre.Rd:11: Lost braces
    11 |     \item{\code{roof_tile}}{a numeric vector, roof_tile}{dummy, roof made out of tiles =1}
       |                                                         ^
checkRd: (-1) hvidovre.Rd:25: Lost braces
    25 |     \item{\code{railways}}{a numeric vector, railways}{distance to nearest railway in meters}
       |                                                       ^
checkRd: (-1) hvidovre.Rd:26: Lost braces
    26 |     \item{\code{nature_SLD}}{a numeric vector, nature_SLD}{distance to nearest nature area in meters}
       |                                                           ^
Error(s) in re-building vignettes:
--- re-building 'Logging.Rmd' using rmarkdown
! Package pdftex.def Error: File `04e371b865d103adff79e62ddf21110362a86130.png'
 not found: using draft setting.

Error: processing vignette 'Logging.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/ParallelLogger.Rcheck/vign_test/ParallelLogger/vignettes/Logging.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Logging.log for more info.
--- failed re-building 'Logging.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'EGAnet'
checkRd: (-1) returns.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{...}{Other options including {type} which refers to the
       |                                      ^
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) PPS.fit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forbes400.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forbes400.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:9: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) turkey.Rd:11: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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    doc    2.8Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) PAS-package.Rd:30: Lost braces
    30 |     {\code{bin model}}{\cr Zhiqiu Hu, Zhiquan Wang, and Shizhong Xu (2012) An infinitesimal model for quantitative trait genomic value prediction. PloS ONE 7: e41336.}
       |                       ^
installed size is  5.1Mb
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    R      3.5Mb
    data   1.5Mb
installed size is  7.1Mb
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    doc   6.7Mb
checkRd: (-1) plotHeat.Rd:113: Lost braces
   113 | code{\link[patternize]{patPCA}}, as 'one' when visualizing single image or as 'multi' for multi
       |     ^
GNU make is a SystemRequirements.
installed size is 11.1Mb
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    R      8.0Mb
    help   3.0Mb
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    help   3.1Mb
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    R      2.8Mb
    help   3.8Mb
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    R      3.1Mb
    help   3.8Mb
checkRd: (-1) pbd_loglik.Rd:31: Lost braces
    31 |     \code{pars2[1]} {set the conditioning on non-extinction of the clade (1) or not (0) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:32: Lost braces
    32 |     \code{pars2[2]} {sets whether the likelihood is for the branching times (0) or the phylogeny (1) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:33: Lost braces
    33 |     \code{pars2[3]} {sets whether the first element of the branching times is the stem (1) or the crown (2) age \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:34: Lost braces
    34 |     \code{pars2[4]} {sets whether the parameters and likelihood should be shown on screen (1) or not (0) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:35: Lost braces
    35 |     \code{pars2[5]} {sets which method should be used in the ode-solver. Default is 'lsoda'. See package deSolve for details. \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:36: Lost braces
    36 |     \code{pars2[6]}{Sets the lower bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}
       |                    ^
checkRd: (-1) pbd_loglik.Rd:37: Lost braces
    37 |     \code{pars2[7]}{Sets the upper bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}  
       |                    ^
installed size is  5.6Mb
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    lib    2.9Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'PBIRV.Rmd' using rmarkdown
! Package pdftex.def Error: File `c58277004c418437bb632c446a101c21bfa3b0d8.pdf'
 not found: using draft setting.

Error: processing vignette 'PBIRV.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/PBIR.Rcheck/vign_test/PBIR/vignettes/PBIRV.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See PBIRV.log for more info.
--- failed re-building 'PBIRV.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
':::' calls which should be '::':
  'PBSmodelling:::.findSquare' 'PBSmodelling:::.getHiddenEnv'
  'PBSmodelling:::.makeCleanVec' 'PBSmodelling:::.readList.P'
  'PBSmodelling:::.trimWhiteSpace'
  See the note in ?`:::` about the use of this operator.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/PBSddesolve.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.2Mb
installed size is  5.2Mb
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    doc        1.4Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.4Mb
checkRd: (-1) twoby2Calibrate.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:85-86: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) twoby2Calibrate.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:111-116: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 11.8Mb
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    libs   8.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) PCM_ABC.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:108-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:114: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) PCM_ABC.Rd:229-231: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:232: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) PCM_ABC.Rd:234: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:235: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) PCM_ABC.Rd:237: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) PCM_ABC.Rd:239: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:240: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:67: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using rmarkdown
! Package pdftex.def Error: File `807b917787d0ecb1f69d2c99ccd243d839c1a908.pdf'
 not found: using draft setting.

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/pcSteiner.Rcheck/vign_test/pcSteiner/vignettes/tutorial.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See tutorial.log for more info.
--- failed re-building 'tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) pcvpcr.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
checkRd: (-1) pcvpls.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
Package suggested but not available for checking: 'cmdstanr'
Package suggested but not available for checking: 'PythonInR'
installed size is 20.3Mb
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    libs    7.4Mb
    share  12.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) embedded.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) embedded.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) ensemble.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) ensemble.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) staged.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) staged.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'ggplot2'
A package should be listed in only one of these fields.
'LazyData' is specified without a 'data' directory
checkRd: (-1) variogramGuess.Rd:94: Lost braces
    94 | Method \code{"b"} was proposed by \doi{10.1016/0098-3004(95)00095-X}{Jian et al. (1996)} and
       |                                                                     ^
checkRd: (-1) variogramGuess.Rd:98: Lost braces
    98 | \doi{10.1016/j.cageo.2008.10.011}{Hiemstra et al. (2009)}.
       |                                  ^
checkRd: (-1) variogramGuess.Rd:100: Lost braces
   100 | Method \code{"d"} was developed by \doi{10.1007/s11004-012-9434-1}{Desassis & Renard (2012)}.
       |                                                                   ^
Running examples in 'peermodels-Ex.R' failed
The error most likely occurred in:

> ### Name: handshake
> ### Title: checks to see if a model is available on the cloud server
> ### Aliases: handshake
> 
> ### ** Examples
> 
> handshake("accept")
Error in `resp_body_json()`:
! Unexpected content type "text/html".
• Expecting type "application/json" or suffix "json".
Backtrace:
    ▆
 1. ├─peermodels::handshake("accept")
 2. │ └─res %>% resp_body_json()
 3. └─httr2::resp_body_json(.)
 4.   └─httr2::resp_check_content_type(...)
 5.     └─httr2:::check_content_type(...)
 6.       └─cli::cli_abort(...)
 7.         └─rlang::abort(...)
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   3.7Mb
Error(s) in re-building vignettes:
--- re-building 'buildmer.Rmd' using rmarkdown
! Package pdftex.def Error: File `0348761f2c90a3b708f4cb3976f7fa6f96594ee1.pdf'
 not found: using draft setting.

Error: processing vignette 'buildmer.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/permutes.Rcheck/vign_test/permutes/vignettes/buildmer.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See buildmer.log for more info.
--- failed re-building 'buildmer.Rmd'

--- re-building 'permutes.Rmd' using rmarkdown
[WARNING] Citeproc: citation oddball not found
! Package pdftex.def Error: File `0df00d50824ed8a41bd7365dc4f38675c817ea2b.pdf'
 not found: using draft setting.

Error: processing vignette 'permutes.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/permutes.Rcheck/vign_test/permutes/vignettes/permutes.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See permutes.log for more info.
--- failed re-building 'permutes.Rmd'

SUMMARY: processing the following files failed:
  'buildmer.Rmd' 'permutes.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) DTV.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown_notangle
! Package pdftex.def Error: File `f90e436221651704be7c1820f5189d66aa0013c8.pdf'
 not found: using draft setting.

Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/PGRdup.Rcheck/vign_test/PGRdup/vignettes/Introduction.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Introduction.log for more info.
--- failed re-building 'Introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    application   4.8Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   1.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
checkRd: (-1) 11_d.init.method.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:24-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:27-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:31-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:29: Lost braces in \itemize; meant \describe ?
'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: 'semPlot'
installed size is  5.5Mb
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    data   1.6Mb
    doc    2.1Mb
checkRd: (-1) pa-internal.Rd:11: Lost braces
    11 | code{l2df}: convert list to data.frame
       |     ^
checkRd: (-1) pa-internal.Rd:14: Lost braces
    14 | code{convertTZ}: force a new timezone on datetime
       |     ^
checkRd: (-1) pa-internal.Rd:16: Lost braces
    16 | code{createTime}: create datetime variable
       |     ^
checkRd: (-1) pa-internal.Rd:18: Lost braces
    18 | code{addDayIndex}: create ID_day variable from timestamp
       |     ^
checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) sample2matrix.Rd:15: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sample2matrix.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
installed size is  6.1Mb
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    doc   5.5Mb
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
checkRd: (-1) get_pixels.Rd:27-29: Lost braces
    27 | if (interactive()) {
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) sprinkle_colnames.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sprinkle_colnames.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:63-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:69-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:74-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:78-83: Lost braces in \itemize; meant \describe ?
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
checkRd: (-1) one_design.Rd:125-126: Lost braces
   125 | function serves for the purpose of spot-testing for any pre-specified {n,
       |                                                                       ^
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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    libs         2.5Mb
    tmp_images   1.9Mb
installed size is  7.0Mb
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    data   1.4Mb
    doc    2.4Mb
    libs   1.6Mb
checkRd: (-1) delta2a.Rd:21: Lost braces; missing escapes or markup?
    21 | delta_k = log(a_k - a_{k+1})
       |                       ^
checkRd: (-1) ordprob.mple.Rd:29: Lost braces
    29 | logical. If code{TRUE} all the q variable are assumed to have the same mean.
       |                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plotluck.Rd:129: Lost braces
   129 |  in factors are are shown as a special factor level code{"?"}. They can be
       |                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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    R             1.1Mb
    examples      1.3Mb
    htmlwidgets   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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    R     2.7Mb
    doc   1.8Mb
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein-package.Rd:20: Lost braces
    20 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plu_more.Rd:16: Lost braces; missing escapes or markup?
    16 | Additional arguments are replaced with "{n} more".
       |                                         ^
Package suggested but not available for checking: 'pmartRdata'
checkRd: (-1) PMCMR-deprecated.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                              ^
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                                                         ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                   ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                              ^
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) estimate.functional.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{bw}{function describing bandwidth selection (see ?gmm for alternatives). Standard is that the bandwidth depends on the sample length $T$ by $m(T)=T^{1/5}$.}
       |                                                                                                                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pois.fe.robust.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:48: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) pois.fe.robust.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
installed size is  5.1Mb
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    libs   1.3Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      6.3Mb
    data   4.3Mb
checkRd: (-1) inputData.Rd:94: Lost braces
    94 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) inputData.Rd:95: Lost braces
    95 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) preprocessData.Rd:81: Lost braces
    81 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) preprocessData.Rd:82: Lost braces
    82 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) stat_quantile_prob.Rd:14: Lost braces; missing escapes or markup?
    14 | Number {25, 50, 75}
       |        ^
installed size is  5.8Mb
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    libs      1.2Mb
checkRd: (-1) MLM_Model.Rd:31: Lost braces; missing escapes or markup?
    31 |   the weight vectors \bold{{w}^{i}} corresponds to class \eqn{i}{i}.
       |                                ^
checkRd: (-1) MLM_Model.Rd:33: Lost braces; missing escapes or markup?
    33 | We set \eqn{{\bold{{w}}^{h}} = 0} and the parameters to be learned are the weight vectors \bold{{w}^{i}}
       |                                                                                                     ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    doc   4.7Mb
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(PopPsiSeqR)
  > 
  > test_check("PopPsiSeqR")
  Saving _problems/test-plot-26.R
  Saving _problems/test-plot-27.R
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot.R:26:5'): returns a plot ────────────────────────────────
  Expected `mock.plot <- windowedFrequencyShift.plotter(mock_data)` not to throw any errors.
  Actually got a <simpleError> with message:
    invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
  ── Error ('test-plot.R:27:5'): returns a plot ──────────────────────────────────
  Error in `eval(code, test_env)`: object 'mock.plot' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_true(ggplot2::is.ggplot(mock.plot@ggplot)) at test-plot.R:27:5
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─ggplot2::is.ggplot(mock.plot@ggplot)
   5.   └─ggplot2::is_ggplot(x)
   6.     └─S7::S7_inherits(x, class_ggplot)
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
  Error:
  ! Test failures.
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'PopPsiSeq_and_Helpers.Rmd' using rmarkdown

Quitting from PopPsiSeq_and_Helpers.Rmd:120-124 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
---
Backtrace:
     x
  1. +-ggplot2::autoplot(...)
  2. \-ggbio::autoplot(...)
  3.   \-ggbio (local) .local(object, ...)
  4.     +-BiocGenerics::do.call(ggplot, c(list(data = object), list(aes.res)))
  5.     +-base::do.call(ggplot, c(list(data = object), list(aes.res)))
  6.     +-ggplot2 (local) `<fn>`(data = `<GRanges>`, `<ggplt2::>`)
  7.     \-ggbio:::ggplot.Vector(data = `<GRanges>`, `<ggplt2::>`)
  8.       \-ggbio::GGbio(gg, data = data)
  9.         +-BiocGenerics::do.call(...)
 10.         +-base::do.call(...)
 11.         \-methods (local) `<fn>`(...)
 12.           +-methods::initialize(value, ...)
 13.           \-methods::initialize(value, ...)
 14.             \-methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'PopPsiSeq_and_Helpers.Rmd' failed with diagnostics:
invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
--- failed re-building 'PopPsiSeq_and_Helpers.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Missing or unexported object: 'CVXR::solve'
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (requireNamespace("testthat", quietly = TRUE)) {
  +   library(testthat)
  +   library(PortfolioTesteR)
  +   test_check("PortfolioTesteR")
  + } else {
  +   message("Skipping tests: 'testthat' not installed")
  + }
  Saving _problems/test-ml-helpers-101.R
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 55 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-optimization.R:2:3', 'test-optimization.R:46:3',
    'test-walk-forward.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ml-helpers.R:92:3'): backtest invariants hold on active dates (smoke, linear) ──
  Error in `.roll_align_common(c(features_list, list(label)))`: No common dates across panels.
  Backtrace:
      ▆
   1. └─PortfolioTesteR::ml_backtest(...) at test-ml-helpers.R:92:3
   2.   └─PortfolioTesteR::roll_fit_predict(...)
   3.     └─PortfolioTesteR:::.roll_align_common(c(features_list, list(label)))
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 55 ]
  Error:
  ! Test failures.
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'Getting_Started_Advanced.Rmd' using rmarkdown

Quitting from Getting_Started_Advanced.Rmd:84-108 [baseline_pooled]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.roll_align_common()`:
! No common dates across panels.
---
Backtrace:
    ▆
 1. └─PortfolioTesteR::ml_backtest(...)
 2.   └─PortfolioTesteR::roll_fit_predict(...)
 3.     └─PortfolioTesteR:::.roll_align_common(c(features_list, list(label)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Getting_Started_Advanced.Rmd' failed with diagnostics:
No common dates across panels.
--- failed re-building 'Getting_Started_Advanced.Rmd'

--- re-building 'getting-started.Rmd' using rmarkdown
--- finished re-building 'getting-started.Rmd'

--- re-building 'optimization-walkforward.Rmd' using rmarkdown
--- finished re-building 'optimization-walkforward.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
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    libs   5.0Mb
installed size is 47.8Mb
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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
Error(s) in re-building vignettes:
--- re-building 'POSTm_vignette.Rmd' using rmarkdown
! Package pdftex.def Error: File `cd68707c92ed76e1ca1aaef4120d6f9941e8e0d5.pdf'
 not found: using draft setting.

Error: processing vignette 'POSTm_vignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/POSTm.Rcheck/vign_test/POSTm/vignettes/POSTm_vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See POSTm_vignette.log for more info.
--- failed re-building 'POSTm_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) coalesce_xy.Rd:22: Lost braces; missing escapes or markup?
    22 | the \code{conflict} argument of {powerjoin}'s join functions. \code{coalesce_xy()} is
       |                                 ^
checkRd: (-1) power_left_join.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{by}{As in {dplyr}, but extended so user can supply a formula or a list
       |                 ^
checkRd: (-1) power_left_join.Rd:79: Lost braces; missing escapes or markup?
    79 | \item{keep}{A boolean for compatibility with {dplyr}, or a value among "left",
       |                                              ^
checkRd: (-1) preprocess_inputs.Rd:37: Lost braces; missing escapes or markup?
    37 | only be used in the \code{x} and \code{y} arguments of {powerjoin} join functions. No
       |                                                        ^
installed size is  6.6Mb
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    doc   6.2Mb
Package suggested but not available for checking: 'MBESS'
Running examples in 'pplot-Ex.R' failed
The error most likely occurred in:

> ### Name: pplot.t.test
> ### Title: Generate p-plot from a series of data points
> ### Aliases: pplot.t.test
> ### Keywords: utilities
> 
> ### ** Examples
> 
> # Show p-plot for significant test (the simulation 
> # has a power of > 88% to return a significant 
> # effect).
> testdata <- rnorm(64, mean = 0.4, sd = 1)
> pplot.t.test(testdata)
Warning in pplot.t.test(testdata) :
  Package 'MBESS' is not installed but required for computing confidence intervals for effect sizes (for plottype >= 2).
Error in pplot.t.test(testdata) : 
Execution halted
checkRd: (-1) ccp_ppm.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{model}{Determines of model fit is such that there are p_{it}s (model=1) or
       |                                                               ^
checkRd: (-1) curve_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) gaussian_ppmx.Rd:143: Lost braces; missing escapes or markup?
   143 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) gaussian_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) ordinal_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) ordinal_ppmx.Rd:147: Lost braces; missing escapes or markup?
   147 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each sujbects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc  10.5Mb
Running examples in 'PPtreeExt-Ex.R' failed
The error most likely occurred in:

> ### Name: PPtreeExt_split
> ### Title: Projection Pursuit Classification Tree with Random Variable
> ###   Selection
> ### Aliases: PPtreeExt_split
> ### Keywords: tree
> 
> ### ** Examples
> 
> data(penguins)
Warning in data(penguins) : data set 'penguins' not found
> penguins <- na.omit(penguins[, -c(2,7, 8)])
Error: object 'penguins' not found
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) diagnose_expressions.Rd:39: Lost braces
    39 | \item wrapping a function argument in two curly braces (e.g. `{{arg}} > 0) means
       |                                                               ^
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R   3.7Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) dev_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:14: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) preference-package.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:58-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:61-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:26-27: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
--- re-building 'prepplotOverview.Rmd' using rmarkdown
! Package pdftex.def Error: File `3d8d7acb1665153b92d2d7242e6c67e32bb81826.pdf'
 not found: using draft setting.

Error: processing vignette 'prepplotOverview.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/prepplot.Rcheck/vign_test/prepplot/vignettes/prepplotOverview.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See prepplotOverview.log for more info.
--- failed re-building 'prepplotOverview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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checkRd: (-1) prereg_initialize.Rd:20: Lost braces; missing escapes or markup?
    20 | the (pre)registration form specification (in {preregr} format), see the
       |                                              ^
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    23 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
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    26 | For an introduction to working with {preregr} (pre)registrations,
       |                                     ^
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    75 | This function creates an R Markdown template from a {preregr}
       |                                                     ^
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    77 | Sheet holding the (pre)registration form specification (in {preregr}
       |                                                            ^
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    81 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
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installed size is 10.0Mb
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    20 | The user does not put these directly into this function, but rather uses code{ode} in the \code{deSolve} package.
       |                                                                              ^
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    20 | \item{lower.v}{logical, if TRUE the specified percentile.value is the upper limit for the mean (or the median or the mode) at the specified confidence level (percentile). If {FALSE} the specified percentile.value is the lower limit for the mean (or the median or the mode) at the specified confidence level (percentile). The default is FALSE.}
       |                                                                                                                                                                               ^
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installed size is 10.4Mb
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checkRd: (-1) proc.Rd:27: Lost braces in \itemize; meant \describe ?
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Unexported objects imported by ':::' calls:
  'bupaR:::allowed_lifecycles' 'bupaR:::apply_grouped_fun'
  See the note in ?`:::` about the use of this operator.
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    91 |     \code{OSME} \tab Output-oriented scale-mix efficiency score \emph{(code{orientation = "out"})}\cr
       |                                                                            ^
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     9 |                 \item{CD}{}{Character disorder scale score}
       |                            ^
checkRd: (-1) proftools-package.Rd:40: Lost braces
    40 |   by the code{kcachegrind} program available on some operating
       |              ^
installed size is 17.2Mb
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Packages required but not available: 'semPlot', 'semptools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  7.0Mb
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installed size is 26.4Mb
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checkRd: (-1) prolific_prescreener.Rd:254: Lost braces in \itemize; meant \describe ?
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Package suggested but not available for checking: 'cmdstanr'
GNU make is a SystemRequirements.
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checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                  ^
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                                      ^
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    21 | response variable. Vector of length emph{n}, assumed to be quantitative.
       |                                         ^
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    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capital letters 
       |                       ^
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    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capitals letters 
       |                       ^
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     7 | See the {rfeel} package now: http://github.com/ColinFay/rfeel}
       |         ^
checkRd: (-1) proust_sentiments.Rd:20: Lost braces; missing escapes or markup?
    20 | See the {rfeel} package now: http://github.com/ColinFay/rfeel
       |         ^
Package suggested but not available for checking: 'rdt'
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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
installed size is  5.3Mb
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checkRd: (-1) qpc.Rd:43: Lost braces
    43 | S{Sulewski, P. (2020). \emph{Normal Distribution with Plasticizing Component,} Communications in Statistics ? Theory and Method 51(11), 3806-3835.}
       |  ^
checkRd: (-1) data1.Rd:14: Lost braces
    14 | The data set from {AbouRizk, S.M., Halpin, D.W., Wilson, J. R. (1994). \emph{Fitting beta distributions based on sample data.} Journal of Construction Engineering and Management 120(2), 288–305.}
       |                   ^
checkRd: (-1) data2.Rd:14: Lost braces; missing escapes or markup?
    14 | The data set presents the height of 99 five-year-old British boys in cm downloaded from {http://www.mas.ncl.ac.uk/njnsm/medfac/docs/intro.pdf.}
       |                                                                                         ^
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checkRd: (-1) table1.Rd:14: Lost braces
    14 | The first data set from {Sulewski, P. (2017) \emph{A new test for independence in 2x2 contingency tables,} Acta Universitatis Lodziensis. Folia Oeconomica, 4(330), 55–75}
       |                         ^
checkRd: (-1) table3.Rd:14: Lost braces
    14 | The third data set from {Sulewski, P. (2021). \emph{Logarithmic Minimum Test for Independence in Three Way Con-tingency Table of Small Sizes.} Journal of Statistical Computation and Simulation 91(13), 2780-2799}
       |                         ^
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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installed size is  5.1Mb
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checkRd: (-1) PTE_bootstrap_inference.Rd:39-42: Lost braces
    39 |                                                         continuous = function(Xytrain){ #defalt is OLS regression
       |                                                                                       ^
checkRd: (-1) PTE_bootstrap_inference.Rd:43-47: Lost braces
    43 |                                                         incidence = function(Xytrain){ #default is logistic regression
       |                                                                                      ^
checkRd: (-1) PTE_bootstrap_inference.Rd:48-52: Lost braces
    48 |                                                         survival = function(Xytrain){ #default is Weibull regression
       |                                                                                     ^
checkRd: (-1) PTE_bootstrap_inference.Rd:66-68: Lost braces
    66 |                                         function(mod, Xyleftout){
       |                                                                 ^
checkRd: (-1) PTE_bootstrap_inference.Rd:74-77: Lost braces
    74 |                                         function(results, indices_1_1, indices_0_0, indices_0_1, indices_1_0){
       |                                                                                                              ^
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    examples   2.6Mb
Running examples in 'pubh-Ex.R' failed
The error most likely occurred in:

> ### Name: axis_labs
> ### Title: Apply labels from variables to axis-labels in plots.
> ### Aliases: axis_labs
> 
> ### ** Examples
> 
> data(kfm, package = "ISwR")
> require(sjlabelled, quietly = TRUE)

Attaching package: 'sjlabelled'

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

    as_label

> kfm <- kfm |>
+   var_labels(
+     dl.milk = "Breast-milk intake (dl/day)",
+     sex = "Sex",
+     weight = "Child weight (kg)",
+     ml.suppl = "Milk substitute (ml/day)",
+     mat.weight = "Maternal weight (kg)",
+     mat.height = "Maternal height (cm)"
+   )
> 
> kfm |>
+   gf_point(weight ~ dl.milk) |>
+   gf_lm(col = 2, interval = "confidence", col = 2) |>
+   axis_labs()
Warning in rep(yes, length.out = len) :
  'x' is NULL so the result will be NULL
Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : 
  replacement has length zero
Calls: axis_labs -> ifelse
Execution halted
checkRd: (-1) ma.Rd:62: Lost braces
    62 | \item{yi}{Numeric vector of length code{k} with observed effect size
       |                                        ^
checkRd: (-1) ma.Rd:65: Lost braces
    65 | \item{vi}{Numeric vector of length code{k} with sampling variances.}
       |                                        ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) plotWordCloud.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{PubMed wordcloud using function 'wordcloud' of package {wordcloud}}
       |                                                               ^
checkRd: (-1) plotWordCloud.Rd:32: Lost braces; missing escapes or markup?
    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                  ^
checkRd: (-1) plotWordCloud.Rd:32: Lost braces; missing escapes or markup?
    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                                           ^
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checkRd: (-1) DataSets.Rd:10: Lost braces; missing escapes or markup?
    10 | \format{the \code{PvarQuantileDF} is a \code{data.frame} with fields \code{prob} an {Qaunt}. 
       |                                                                                     ^
checkRd: (-1) pvlrt.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
checkRd: (-1) r_contin_table_zip.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
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    10 |   \item{listRanef}{{\emph{ranef(model)}} object where {\emph{model}} is an { \emph{lmer}} object.}
       |                                                                            ^
installed size is 13.8Mb
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) qmethod-package.Rd:109: Lost braces
   109 |   \item Van Exel, J., and G. de Graaf, 2005. \emph{Q Methodology: A Sneak Preview}\cr \url{https://qmethodblog.files.wordpress.com/2016/01/qmethodologyasneakpreviewreferenceupdate.pdf}{Available at this link}.
       |                                                                                                                                                                                         ^
checkRd: (-1) qmethod-package.Rd:110: Lost braces
   110 |   \item Brown, S. R., 1980. \emph{Political subjectivity: Applications of Q methodology in political science}, New Haven, CT: Yale University Press.\cr \url{https://qmethodblog.files.wordpress.com/2016/01/brown-1980-politicalsubjectivity.pdf}{Available at this link}.
       |                                                                                                                                                                                                                                                   ^
checkRd: (-1) hideLocation.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{trueLoc}{A vector of one or more numbers in the set {1, 2, ..., nSubjects} whose locations are to be hidden.}
       |                                                           ^
checkRd: (-1) hideLocation.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{nSubjects}{An integer larger than 1 used to define the set {1, 2, ..., nSubjects}.}
       |                                                                  ^
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GNU make is a SystemRequirements.
installed size is 12.6Mb
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'QTE_RD.Rmd' using rmarkdown
Error reading bibliography file qte_rdd.bib:
(line 11, column 3):
unexpected '%'
expecting white space
Error: processing vignette 'QTE_RD.Rmd' failed with diagnostics:
pandoc document conversion failed with error 25
--- failed re-building 'QTE_RD.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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installed size is 10.2Mb
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checkRd: (-1) IPWE_mean_IndCen.Rd:54-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) simJLSDdata.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{case}{string. One of {"a", "b", "c"}, corresponding to three models.}
       |                            ^
checkRd: (-1) simJLSDdata.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) als_data.Rd:27: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) als_data_qc_mapping.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:13: Lost braces in \itemize; meant \describe ?
installed size is  5.3Mb
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checkRd: (-1) quarries.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:20-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:26-28: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
--- re-building 'build.Rmd' using rmarkdown
--- finished re-building 'build.Rmd'

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

--- re-building 'data-sources.Rmd' using rmarkdown
--- finished re-building 'data-sources.Rmd'

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

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

--- re-building 'tools.Rmd' using rmarkdown
File ../reference/figures/quickstart-filter.png not found in resource path
Error: processing vignette 'tools.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'tools.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' 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
installed size is  5.3Mb
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checkRd: (-1) est.R0.ML.Rd:98: Lost braces
    98 | Supplementary Material S1 from \doi{10.1186/1472-6947-12-147}{Obadia et al., 2012}.
       |                                                              ^
checkRd: (-1) plot.R0.R.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from one estimation method.
       |                                                      ^
checkRd: (-1) plot.R0.sR.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from an
       |                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) do_admb.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) do_admb.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) do_admb.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_pars.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: 'ReGenesees'
GNU make is a SystemRequirements.
installed size is  5.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'bootmlm'
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.
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'
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
checkRd: (-1) r4ss-package.Rd:9: Lost braces; missing escapes or markup?
     9 | A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.19.01, from April 2022).
       |                                                                                                                                                                                                                                                                                                                                                                                                ^
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   3.9Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'using_R6causal.Rmd' using rmarkdown
! Package pdftex.def Error: File `3e34015c146dfdb256070bb6c95db05ae0b5dc6c.pdf'
 not found: using draft setting.

Error: processing vignette 'using_R6causal.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/R6causal.Rcheck/vign_test/R6causal/vignettes/using_R6causal.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See using_R6causal.log for more info.
--- failed re-building 'using_R6causal.Rmd'

SUMMARY: processing the following file failed:
  'using_R6causal.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) extract_class.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extract_class.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extract_class.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) post_RA_fits.Rd:61: Lost braces; missing escapes or markup?
    61 |     \item{\code{H(po_{bm_{n.bm}}, po_act)}:}{ last benchmark prior bm_{n.bm} inducing the fit \code{fits.bm[[n.bm]]} and actual prior}
       |                                                                       ^
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    6.6Mb
    libs   1.0Mb
'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          2.1Mb
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'RandomForestsGLS_user_guide.Rmd' using rmarkdown
! Package pdftex.def Error: File `701162a179fd612371dd804fd56d34d5acd43af7.pdf'
 not found: using draft setting.

Error: processing vignette 'RandomForestsGLS_user_guide.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/RandomForestsGLS.Rcheck/vign_test/RandomForestsGLS/vignettes/RandomForestsGLS_user_guide.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See RandomForestsGLS_user_guide.log for more info.
--- failed re-building 'RandomForestsGLS_user_guide.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) makeDesignMatrix.Rd:16: Lost braces; missing escapes or markup?
    16 | is randomized to a certain treatment {j}, the entry of \code{(i,j)} of the
       |                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) grottaBar.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rankL2R.Rd:18: Lost braces; missing escapes or markup?
    18 | where the vector dimension is 2^{response.number}.}
       |                                 ^
Auto-generated content requiring editing in Rd file 'RApiDatetime-package.Rd':
  \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
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      1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'RaSEn-demo.Rmd' using rmarkdown
! Package pdftex.def Error: File `f67b1baed3943fb96d8f6498943603b6ca04bb50.pdf'
 not found: using draft setting.

Error: processing vignette 'RaSEn-demo.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/RaSEn.Rcheck/vign_test/RaSEn/vignettes/RaSEn-demo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See RaSEn-demo.log for more info.
--- failed re-building 'RaSEn-demo.Rmd'

SUMMARY: processing the following file failed:
  'RaSEn-demo.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    libs   1.4Mb
Error(s) in re-building vignettes:
--- re-building 'Intro_on_the_package.Rmd' using rmarkdown
! Package pdftex.def Error: File `f769fce833cde68c6f69e009d7b5be0128e24963.pdf'
 not found: using draft setting.

Error: processing vignette 'Intro_on_the_package.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/ratematrix.Rcheck/vign_test/ratematrix/vignettes/Intro_on_the_package.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Intro_on_the_package.log for more info.
--- failed re-building 'Intro_on_the_package.Rmd'

--- re-building 'Making_prior_on_ratematrix.Rmd' using rmarkdown
! Package pdftex.def Error: File `649f71c257e82c9ffa90653fd8c25fb5087de12c.pdf'
 not found: using draft setting.

Error: processing vignette 'Making_prior_on_ratematrix.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/ratematrix.Rcheck/vign_test/ratematrix/vignettes/Making_prior_on_ratematrix.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Making_prior_on_ratematrix.log for more info.
--- failed re-building 'Making_prior_on_ratematrix.Rmd'

--- re-building 'Set_custom_starting_point.Rmd' using rmarkdown
! Package pdftex.def Error: File `231a4d08e13bba0753a58031d639ee059a0111ae.pdf'
 not found: using draft setting.

Error: processing vignette 'Set_custom_starting_point.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/ratematrix.Rcheck/vign_test/ratematrix/vignettes/Set_custom_starting_point.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Set_custom_starting_point.log for more info.
--- failed re-building 'Set_custom_starting_point.Rmd'

SUMMARY: processing the following files failed:
  'Intro_on_the_package.Rmd' 'Making_prior_on_ratematrix.Rmd'
  'Set_custom_starting_point.Rmd'

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
checkRd: (-1) S1.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{m_bar}{the sample vector of moments for a specified vector $(h_{a,r},y)$}
       |                                                                      ^
checkRd: (-1) S1.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{N_k}{index of the $ h_{a,r}$ function considered}
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    cont  20.1Mb
checkRd: (-1) nc_open_CGLS.Rd:29-32: Lost braces
    29 | if(resolution == "300m"){
       |                         ^
checkRd: (-1) nc_open_CGLS.Rd:33-36: Lost braces
    33 | if(resolution == "1km"){
       |                        ^
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Rchoice.Rd:159: Lost braces; missing escapes or markup?
   159 |  \code{ranp}. If the parameters are assumed to be normally distributed \eqn{\beta_i ~ N(\beta, \Sigma)}, then the random parameter are constructed as: \deqn{\beta_{ir}=\beta+L\omega_{ir}} where \eqn{LL'=\Sigma} and \eqn{\omega_{ir}} is the {r}-th draw from standard normal distribution for individual \eqn{i}. 
       |                                                                                                                                                                                                                                                 ^
Error(s) in re-building vignettes:
--- re-building 'binary_variables_tutorial.rmd' using rmarkdown
--- finished re-building 'binary_variables_tutorial.rmd'

--- re-building 'do_not_impute_matrix.rmd' using rmarkdown
--- finished re-building 'do_not_impute_matrix.rmd'

--- re-building 'impute_with_saved_model.rmd' using rmarkdown
--- finished re-building 'impute_with_saved_model.rmd'

--- re-building 'optunadb.rmd' using rmarkdown
--- finished re-building 'optunadb.rmd'

--- re-building 'summary_functions.rmd' using rmarkdown
--- finished re-building 'summary_functions.rmd'

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

--- re-building 'virtual_environment_tutorial.rmd' using rmarkdown
--- finished re-building 'virtual_environment_tutorial.rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: '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
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Rcplex.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.8Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    include  13.5Mb
    libs      1.2Mb
installed size is 39.7Mb
  sub-directories of 1Mb or more:
    include  38.1Mb
    libs      1.4Mb
installed size is 48.7Mb
  sub-directories of 1Mb or more:
    include  48.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    include   9.6Mb
    libs      1.2Mb
installed size is 327.3Mb
  sub-directories of 1Mb or more:
    dic   325.5Mb
    libs    1.7Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.1Mb
GNU make is a SystemRequirements.
installed size is 52.2Mb
  sub-directories of 1Mb or more:
    libs  50.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    include   2.2Mb
    libs      1.3Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    include        8.6Mb
    jsonexamples   3.8Mb
    libs           2.0Mb
Found the following significant warnings:
  tskit/kastore.c:1157:32: warning: unknown conversion type character 'z' in format [-Wformat=]
  tskit/kastore.c:1157:18: warning: too many arguments for format [-Wformat-extra-args]
  tskit/kastore.c:1158:32: warning: unknown conversion type character 'z' in format [-Wformat=]
  tskit/kastore.c:1158:18: warning: too many arguments for format [-Wformat-extra-args]
  tskit/kastore.c:1165:40: warning: unknown conversion type character 'z' in format [-Wformat=]
  tskit/kastore.c:1165:53: warning: unknown conversion type character 'z' in format [-Wformat=]
  tskit/kastore.c:1165:62: warning: format '%p' expects argument of type 'void *', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  tskit/kastore.c:1165:13: warning: unknown conversion type character 'z' in format [-Wformat=]
  tskit/kastore.c:1165:13: warning: format '%p' expects argument of type 'void *', but argument 7 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  tskit/kastore.c:1165:13: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.4/RcppTskit.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'g++.exe (GCC) 13.3.0'
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'RDHonest.Rmd' using rmarkdown
! Package pdftex.def Error: File `c8009755bd8f28358e123a694873d467df0ab6a8.pdf'
 not found: using draft setting.

Error: processing vignette 'RDHonest.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/RDHonest.Rcheck/vign_test/RDHonest/vignettes/RDHonest.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See RDHonest.log for more info.
--- failed re-building 'RDHonest.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) farthest_point_sampling.Rd:28: Lost braces; missing escapes or markup?
    28 | space P = {p_1, ..., p_k}, such that each p_i is the farthest 
       |           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) computeCBMeasure.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:56: Lost braces in \itemize; meant \describe ?
'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:
    duckhts_extension   3.5Mb
    extdata             1.7Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    data   1.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) ReAD.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
checkRd: (-1) em_hmm.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Automotive.Rd:29: Lost braces
    29 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). Own postprocessing.
       |                                                           ^
checkRd: (-1) Automotive.Rd:33: Lost braces
    33 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). 
       |                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
checkRd: (-1) recombinator.Rd:32-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) recombinator.Rd:35-38: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) pseudo.geefit.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.geefit.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   1.2Mb
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    redengine  28.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.0Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.8Mb
checkRd: (-1) make_refreshable.Rd:13: Lost braces
    13 | not that quotes need to be escaped (code{\"}).}
       |                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) impute_down_nuts.Rd:21: Lost braces
    21 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
checkRd: (-1) validate_data_frame.Rd:19: Lost braces
    19 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) fbase1.binomial.Rd:32: Lost braces; missing escapes or markup?
    32 | In all base log-likelihood functions, we have dropped any additive terms that are independent of the distribution parameter, e.g. constant terms or those terms that are dependent on the response variable only. This is done for computational efficiency. Therefore, these functions cannot be used to obtain the absolute values of log-likelihood functions but only in the context of optimization and/or sampling. Users can write thin wrappers around these functions to add the constant terms to the function value. (Derivatives do not need correction. For binomial family, all factorial terms are ignored since they only depend on \code{n} and {y}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
Package suggested but not available for checking: 'semPlot'
Error(s) in re-building vignettes:
--- re-building 'short_intro.Rmd' using knitr

Quitting from short_intro.Rmd:44-46 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'semPlot'
---
Backtrace:
    ▆
 1. └─base::loadNamespace(x)
 2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 3.     └─base (local) withOneRestart(expr, restarts[[1L]])
 4.       └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'short_intro.Rmd' failed with diagnostics:
there is no package called 'semPlot'
--- 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
Package which this enhances but not available for checking: 'Rcplex'
checkRd: (-1) polarizacion_Dalton.Rd:26: Lost braces; missing escapes or markup?
    26 | {Pd = sqrt(sum(p_j*(x_j-mean(x_p))/4.5)^2)}
       | ^
checkRd: (-1) reparto_div.Rd:37: Lost braces; missing escapes or markup?
    37 | The set of divisors is formed by the odd numbers, that is {1,3,..,2n+1}.
       |                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) rem.dyad.Rd:121: Lost braces; missing escapes or markup?
   121 | \item Single or multiple covariates, time varying: For \code{CovSnd}, \code{CovRec}, or \code{CovInt}, an \code{m} by \code{p} by {n} array whose respective dimensions index time (i.e., event number), covariate, and actor.  For \code{CovEvent}, a \code{m} by \code{p} by \code{n} by \code{n} array, whose dimensions are analogous to the previous case.
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) twosidedPValuestobins.Rd:84: Lost braces; missing escapes or markup?
    84 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
checkRd: (-1) ztobins.Rd:90: Lost braces; missing escapes or markup?
    90 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) method.A.Rd:200-205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:206-211: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:231-236: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:237-242: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:201-206: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:207-212: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:232-237: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:238-243: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'reportRmd.Rmd' using rmarkdown
File images/forestmv_unadj.png not found in resource path
Error: processing vignette 'reportRmd.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'reportRmd.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) NCBirths2004.Rd:16: Lost braces
    16 |     \item{\code{Smoker}}{Mother a smoker? code{No}, \code{Yes}}
       |                                               ^
checkRd: (-1) ExpandProbs.Rd:35: Lost braces; missing escapes or markup?
    35 |      {z_probs2 sqrt((n-1)/n) = t_probs,n-1}
       |      ^
GNU make is a SystemRequirements.
checkRd: (-1) resistance.Rd:52: Lost braces
    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs      1.7Mb
    models    1.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    reveal.js-4.2.1   4.9Mb
checkRd: (-1) saveRev.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{use_wd}{logical - If TRUE, the history will be prepended by setwd({'users current working directory'}). This function will set the script's working directory to
       |                                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   4.8Mb
    help   1.1Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data  13.3Mb
Error(s) in re-building vignettes:
--- re-building 'FAQ.Rmd' using rmarkdown_notangle
--- finished re-building 'FAQ.Rmd'

--- re-building 'Targets.Rmd' using rmarkdown_notangle
--- finished re-building 'Targets.Rmd'

--- re-building 'UseCase1.Rmd' using rmarkdown_notangle
! Package pdftex.def Error: File `d0aea531ab8bf192d97339984f0482d616cf0be9.pdf'
 not found: using draft setting.

Error: processing vignette 'UseCase1.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/rflsgen.Rcheck/vign_test/rflsgen/vignettes/UseCase1.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See UseCase1.log for more info.
--- failed re-building 'UseCase1.Rmd'

--- re-building 'UseCase2.Rmd' using rmarkdown_notangle
! Package pdftex.def Error: File `f463efada7808d77208b373b6e4b4d241bbd745f.png'
 not found: using draft setting.

Error: processing vignette 'UseCase2.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/rflsgen.Rcheck/vign_test/rflsgen/vignettes/UseCase2.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See UseCase2.log for more info.
--- failed re-building 'UseCase2.Rmd'

--- re-building 'UseCase3.Rmd' using rmarkdown_notangle
! Package pdftex.def Error: File `7133fb34bd2d5289b5664d5670bed619739e4379.png'
 not found: using draft setting.

Error: processing vignette 'UseCase3.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/rflsgen.Rcheck/vign_test/rflsgen/vignettes/UseCase3.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See UseCase3.log for more info.
--- failed re-building 'UseCase3.Rmd'

SUMMARY: processing the following files failed:
  'UseCase1.Rmd' 'UseCase2.Rmd' 'UseCase3.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.0Mb
checkRd: (-1) GenDataPopulation.Rd:21: Lost braces
    21 | {data}{Population of data}
       |       ^
checkRd: (-1) GenDataSample.Rd:23: Lost braces
    23 | {data}{Sample of data}
       |       ^
'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) RiemannianMetric.Rd:450-453: Lost braces
   450 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:484-487: Lost braces
   484 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:588-591: Lost braces
   588 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) Ghana_2021_school_attendance.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Ghana_2021_school_attendance_geometry.Rd:75: Lost braces in \itemize; meant \describe ?
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc     7.2Mb
    fonts   1.5Mb
    libs    2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) code_sawtooth_design.Rd:53: Lost braces
    53 | /url{http://www.sawtoothsoftware.com/help/lighthouse-studio/manual/index.html?hid_web_cbc_exporting.html}
       |     ^
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
checkRd: (-1) rhandsontable-package.Rd:8: Lost braces
     8 | R interface for creating tables using Handsontable, url{https://handsontable.com/}
       |                                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) GenerateClusterData.Rd:34: Lost braces; missing escapes or markup?
    34 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2},
       |                                                ^
checkRd: (-1) GenerateClusterData.Rd:35: Lost braces; missing escapes or markup?
    35 | -v_{(numberOfClusters-1)/2} (if \code{numberOfClusters} is odd)
       |    ^
checkRd: (-1) GenerateClusterData.Rd:36: Lost braces; missing escapes or markup?
    36 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2}
       |                                                ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:25-26: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:27-28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:29-30: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:31-32: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:33-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:35-36: Lost braces
    35 |    \item{pam_cluster_64_7_5715},{N=64, seven clusters with 5715 vectors per
       |                                 ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:37-38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:39-40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
Found the following significant warnings:
  ../inst/include/ribios_arg.h:23:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  argparse.c:62:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/ribiosArg.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
Found the following significant warnings:
  log.c:378:39: warning: unknown conversion type character 'T' in format [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/ribiosIO.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
Package which this enhances but not available for checking: 'Vennerable'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc       7.3Mb
    extdata   3.2Mb
    libs      1.2Mb
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
checkRd: (-1) iex.chart.Rd:23: Lost braces; missing escapes or markup?
    23 | r takes only of of the values accepted IN API request. {"5y", "2y", "1y", "ytd", "6m", "3m", "1m", "1d"}
       |                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    models   6.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    lib    3.1Mb
    libs   3.8Mb
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(riskmetric)
  > 
  > options(repos = "fake-cran.fake-r-project.org")
  > 
  > test_check("riskmetric")
  Execution halted
checkRd: (-1) riskParityPortfolio.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       | ^
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |     ^
checkRd: (-1) riskPredict.Rd:38: Lost braces; missing escapes or markup?
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       | ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |     ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                      ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                             ^
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                                                                   ^
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:
  src/jri/src/Makefile.win
  src/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 '_exit', possibly from '_exit' (C)
  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.
Error(s) in re-building vignettes:
--- re-building 'rjd3bench.Rmd' using rmarkdown

Quitting from rjd3bench.Rmd:98-131 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.jcall()`:
! RcallMethod: cannot determine object class
---
Backtrace:
    ▆
 1. └─rjd3bench::temporal_disaggregation(Y, indicators = x)
 2.   └─rjd3toolkit::.r2jd_tsdata(series)
 3.     └─rJava::.jcall(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'rjd3bench.Rmd' failed with diagnostics:
RcallMethod: cannot determine object class
--- failed re-building 'rjd3bench.Rmd'

SUMMARY: processing the following file failed:
  'rjd3bench.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
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Error(s) in re-building vignettes:
--- re-building 'rjdmarkdown-html.Rmd' using rmarkdown
--- finished re-building 'rjdmarkdown-html.Rmd'

--- re-building 'rjdmarkdown-pdf.Rmd' using rmarkdown
! Package pdftex.def Error: File `9db2367531cea3219469353655881b4a69bf12e3.pdf'
 not found: using draft setting.

Error: processing vignette 'rjdmarkdown-pdf.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/rjdmarkdown.Rcheck/vign_test/rjdmarkdown/vignettes/rjdmarkdown-pdf.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See rjdmarkdown-pdf.log for more info.
--- failed re-building 'rjdmarkdown-pdf.Rmd'

SUMMARY: processing the following file failed:
  'rjdmarkdown-pdf.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
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    include   3.4Mb
    libs      3.6Mb
installed size is 12.1Mb
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    java  12.0Mb
installed size is 10.8Mb
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installed size is 10.3Mb
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'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
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    extdata  23.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    lemon   2.9Mb
    libs    2.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
GNU make is a SystemRequirements.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    include   7.5Mb
    lib       3.1Mb
    libs      5.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rnaturalearthhires'
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
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    rmd   5.9Mb
checkRd: (-1) setOption.Matlab.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setOption.Matlab.Rd:40-41: Lost braces in \itemize; meant \describe ?
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'bridgestan'
Package suggested but not available for checking: 'cmdstanr'
installed size is  5.0Mb
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    libs   4.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'semPlot'
Missing link or links in Rd file 'LFD.Rd':
  'plot.H_LFD '

See section 'Cross-references' in the 'Writing R Extensions' manual.
checkRd: (-1) histMisclassif.Rd:22: Lost braces
    22 | err_i = 1 - max_{k={1,\ldots,K}} P(Z_i=k|x_i)
       |                 ^
checkRd: (-1) histMisclassif.Rd:22: Lost braces
    22 | err_i = 1 - max_{k={1,\ldots,K}} P(Z_i=k|x_i)
       |                    ^
checkRd: (-1) nsgaControl.Rd:20-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:28-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:36-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:56: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) myTarGetClientList.Rd:33: Lost braces
    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
Error(s) in re-building vignettes:
--- re-building 'rnaCrosslinkOO.Rmd' using rmarkdown
File rnaCrosslinkProtocol.jpg not found in resource path
Error: processing vignette 'rnaCrosslinkOO.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'rnaCrosslinkOO.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'rnaturalearthhires'
installed size is 17.1Mb
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checkRd: (-1) nexml_get.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:35: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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    extdata   2.0Mb
    libs      3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.7Mb
checkRd: (-1) fData.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:45-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:49-51: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) outliergram.Rd:55-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:59-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:63-65: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) outliergram.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 11.3Mb
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    R  11.2Mb
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
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    libs   5.4Mb
checkRd: (-1) predict.robu.Rd:36-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.robu.Rd:43-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.robu.Rd:50-55: Lost braces in \itemize; meant \describe ?
Missing or unexported object: 'CVXR::solve'
'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
checkRd: (-1) descriptiveTable.Rd:18: Lost braces
    18 | other object type that does not fail in code{model.frame(object)}.}
       |                                             ^
'LazyData' is specified without 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: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 17.3Mb
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    doc  15.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R         3.2Mb
    extdata   2.7Mb
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
checkRd: (-1) read_ascii.Rd:33: Lost braces
    33 | \item{respondent_pattern}{For use when the file does not contain a line for every card for every respondent (or contains extra lines that correspond to no respondent), a regular expression that matches the file's respondent identifier; e.g., if the respondent number is stored in the first four digits of each line, preceded by a space, "(?<=^\\s)\\d{4}".}
       |                                                                                                                                                                                                                                                                                                                                                               ^
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ROracle.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.7Mb
    libs   1.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      4.9Mb
    help   1.1Mb
    libs   1.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plotImage.blcTree.Rd:17: Lost braces
    17 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
checkRd: (-1) plotImage.glcTree.Rd:16: Lost braces
    16 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.3Mb
checkRd: (-1) get.poetry.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{output}{Can be any or a combination of the input terms {'author', 'title', 'lines', 'linecount'}. If NULL, all
       |                                                              ^
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RPostgreSQL.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  5.4Mb
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    extdata   4.5Mb
Error(s) in re-building vignettes:
--- re-building 'Guide_to_RPPASPACE.Rmd' using rmarkdown_notangle
! Package pdftex.def Error: File `a1f5eada25eb960c163b7652f345b3cbdfe1eddb.png'
 not found: using draft setting.

Error: processing vignette 'Guide_to_RPPASPACE.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/RPPASPACE.Rcheck/vign_test/RPPASPACE/vignettes/Guide_to_RPPASPACE.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Guide_to_RPPASPACE.log for more info.
--- failed re-building 'Guide_to_RPPASPACE.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) as.tg.Rd:18: Lost braces; missing escapes or markup?
    18 | Renames the \code{class(tg)["name"]} attribute and sets {class(tg)["type"] <- "TextGrid"} (if it is not already set)
       |                                                         ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) check_node.Rd:11: Lost braces
    11 | \item{x}{\\code{list}, the node to check}
       |                ^
installed size is  5.5Mb
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    libs   4.1Mb
'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
checkRd: (-1) ex.Rd:20: Lost braces
    20 | Execute a ops-dag using `code{wrap()}` data as values.
       |                              ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                          ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                                                   ^
checkRd: (-1) R2_lik.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{R2_lik()} is also computed for LMMs and GLMMs in the {MuMIn} package.
       |                                                            ^
checkRd: (-1) R2_pred.Rd:32: Lost braces; missing escapes or markup?
    32 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of R2_resid.
       |                                                                                                            ^
checkRd: (-1) R2_resid.Rd:69: Lost braces; missing escapes or markup?
    69 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of \code{R2_resid()}
       |                                                                                                            ^
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
checkRd: (-1) rrecsys.Rd:72: Lost braces; missing escapes or markup?
    72 |  The average deviation rating $dev_{ij}$ between co-rated items is defined by:
       |                                    ^
checkRd: (-1) rrecsys.Rd:76: Lost braces; missing escapes or markup?
    76 |  Where $c_{ij}$ is the number of co-ratings between items $i$ and $j$ and $r_{ui}$ is an existing rating for user $u$ on item $i$. The Weighted Slope One takes into account both, information from users who rated the same item and the number of observed ratings.
       |           ^
checkRd: (-1) rrecsys.Rd:76: Lost braces; missing escapes or markup?
    76 |  Where $c_{ij}$ is the number of co-ratings between items $i$ and $j$ and $r_{ui}$ is an existing rating for user $u$ on item $i$. The Weighted Slope One takes into account both, information from users who rated the same item and the number of observed ratings.
       |                                                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) lateformeeting.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:11: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) regrad.Rd:46: Lost braces; missing escapes or markup?
    46 |  \item \code{x-axis} {1st column: The names of the different institutions}
       |                      ^
checkRd: (-1) regrad.Rd:47: Lost braces; missing escapes or markup?
    47 |  \item \code{y-axis} {2nd column: The value to show completeness}
       |                      ^
Package suggested but not available for checking: 'rnaturalearthhires'
checkRd: (-1) rrinf_clust.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}. See \link{example_clustering} for details.}
       |                                                                                  ^
checkRd: (-1) rrtest_clust.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}.
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) rSCA.modeling.Rd:61: Lost braces; missing escapes or markup?
    61 |                 a predefined string to specify how the information of leaf nodes will be stored in the map file. A full list of options for mapvalue is: {mean, max, min, median, interval, radius, variation, random}. Default value is "mean". Use "interval" to get an interval bounded by the minimum and maximum values, (i.e., [min, max]). The option of "radius" will output the mean and the radius [i.e., (max - min) / 2] at the same time. Use "variation" to output the mean and the standard deviation. The option of "random" will output the information as an interval like the "interval" option, but it will use a random value within the interval as the predicted value.
       |                                                                                                                                                          ^
installed size is  5.4Mb
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'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   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'semPlot'

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
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    4.8Mb
    libs  13.0Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib    1.8Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is 55.7Mb
  sub-directories of 1Mb or more:
    libs    1.0Mb
    swipl  54.4Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   6.4Mb
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                              ^
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                                    ^
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mockery)
  > library(RTD)
  > 
  > test_check("RTD")
  Saving _problems/test-td-65.R
  Saving _problems/test-td-101.R
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 10 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-td.R:65:3'): td_upload works with mock ─────────────────────────
  Error in `file(con, "w")`: cannot open the connection
  Backtrace:
      ▆
   1. └─RTD (local) setup_fake_embulk() at test-td.R:65:3
   2.   └─base::writeLines("@echo off\necho fake embulk", fake_embulk) at test-td.R:17:5
   3.     └─base::file(con, "w")
  ── Error ('test-td.R:101:3'): td_upload works with mock when the table already exists ──
  Error in `file(con, "w")`: cannot open the connection
  Backtrace:
      ▆
   1. └─RTD (local) setup_fake_embulk() at test-td.R:101:3
   2.   └─base::writeLines("@echo off\necho fake embulk", fake_embulk) at test-td.R:17:5
   3.     └─base::file(con, "w")
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 10 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
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    rmarkdown  11.0Mb
GNU make is a SystemRequirements.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   8.5Mb
Codoc mismatches from Rd file 'ADvector.Rd':
\S4method{findInterval}{advector,advector}
  Code: function(x, vec, rightmost.closed = FALSE, all.inside = FALSE,
                 left.open = FALSE)
  Docs: function(x, vec, rightmost.closed = FALSE, all.inside = FALSE,
                 left.open = FALSE, checkSorted = TRUE, checkNA = TRUE)
  Argument names in docs not in code:
    checkSorted checkNA
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
checkRd: (-1) rt_GET.Rd:13: Lost braces
    13 | code{\link[httr]{GET}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
checkRd: (-1) rt_POST.Rd:13: Lost braces
    13 | code{\link[httr]{POST}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.8Mb
GNU make is a SystemRequirements.
checkRd: (-1) rts.Rd:32: Lost braces
    32 | If a name of a raster time series file is provided for the \code{x} argument, it acts the same as code{\link[rts]{read.rts}}.
       |                                                                                                       ^
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^
Package which this enhances but not available for checking: 'glmmADMB'
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                ^
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                                   ^
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 10.7Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs      5.2Mb
checkRd: (-1) HardThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
checkRd: (-1) SoftThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    bin  10.1Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    include   1.3Mb
    libs      4.8Mb
Package suggested but not available for checking: 'unix'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                   ^
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                                 ^
checkRd: (-1) ZigZagLogistic.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{dataY}{Vector of length n containing {0, 1}-valued observations of the dependent variable y.}
       |                                            ^
Error(s) in re-building vignettes:
--- re-building 'zooroh-vignette.Rmd' using rmarkdown
! Package pdftex.def Error: File `62aeb0f6c4f979fe3124502809c501c0dad7e77d.pdf'
 not found: using draft setting.

Error: processing vignette 'zooroh-vignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/RZooRoH.Rcheck/vign_test/RZooRoH/vignettes/zooroh-vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See zooroh-vignette.log for more info.
--- failed re-building 'zooroh-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Possible_warnings_of_sampbias.Rmd' using rmarkdown
--- finished re-building 'Possible_warnings_of_sampbias.Rmd'

--- re-building 'Using_the_samp_bias_rpackage.Rmd' using rmarkdown
! Package pdftex.def Error: File `b3fa20398a48b18b9924fac38ed58f49d830bd4e.png'
 not found: using draft setting.

Error: processing vignette 'Using_the_samp_bias_rpackage.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/sampbias.Rcheck/vign_test/sampbias/vignettes/Using_the_samp_bias_rpackage.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Using_the_samp_bias_rpackage.log for more info.
--- failed re-building 'Using_the_samp_bias_rpackage.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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      1.4Mb
    libs  13.5Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
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  6.1Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.1Mb
checkRd: (-1) gen.ds.Rd:43-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:50-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:64-65: Lost braces
    64 |    \item{the dependence parameter \code{dep} or the vector of dependence parameters \code{dep}. When missing, these coefficients are obtained from independent standard uniform sampling.
       |         ^
checkRd: (-1) gen.ds.Rd:66: Lost braces
    66 |    \item{the list \code{asy} of asymmetric weights \eqn{\beta_{i,b}} for \eqn{b \in B}  and \eqn{i \in b}. When missing, these coefficients are obtained from independent standard uniform sampling followed by renormalization in order to satisfy the sum-to-one constraints.}
       |         ^
'LazyData' is specified without 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) setData.ReducedRankRegressions.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setData.ReducedRankRegressions.Rd:17-18: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'scaper-vignette-CytoSig.Rmd' using rmarkdown
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
! Package pdftex.def Error: File `ec02dfd7afbdbf34ecb6fab00197a77435fd302a.pdf'
 not found: using draft setting.

Error: processing vignette 'scaper-vignette-CytoSig.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/scaper.Rcheck/vign_test/scaper/vignettes/scaper-vignette-CytoSig.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See scaper-vignette-CytoSig.log for more info.
--- failed re-building 'scaper-vignette-CytoSig.Rmd'

--- re-building 'scaper-vignette-Reactome.Rmd' using rmarkdown
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
! Package pdftex.def Error: File `f12efb46c3c7a4b66080cfdde11b7d9ebad2fad9.pdf'
 not found: using draft setting.

Error: processing vignette 'scaper-vignette-Reactome.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/scaper.Rcheck/vign_test/scaper/vignettes/scaper-vignette-Reactome.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See scaper-vignette-Reactome.log for more info.
--- failed re-building 'scaper-vignette-Reactome.Rmd'

SUMMARY: processing the following files failed:
  'scaper-vignette-CytoSig.Rmd' 'scaper-vignette-Reactome.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) scatterD3.Rd:209: Lost braces; missing escapes or markup?
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       | ^
checkRd: (-1) scatterD3.Rd:209: Lost braces
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       |                                              ^
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'scbursts.Rmd' using rmarkdown
! Package pdftex.def Error: File `ef74ae0c3fa62f06803b93ea8475252efe367036.pdf'
 not found: using draft setting.

Error: processing vignette 'scbursts.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/scbursts.Rcheck/vign_test/scbursts/vignettes/scbursts.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See scbursts.log for more info.
--- failed re-building 'scbursts.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Scoper-Vignette.Rmd' using rmarkdown
! Package pdftex.def Error: File `3078b6a2255b7748c529caeac446d4c0b2b9dc37.pdf'
 not found: using draft setting.

Error: processing vignette 'Scoper-Vignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/scoper.Rcheck/vign_test/scoper/vignettes/Scoper-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Scoper-Vignette.log for more info.
--- failed re-building 'Scoper-Vignette.Rmd'

SUMMARY: processing the following file failed:
  'Scoper-Vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    cppad     9.5Mb
    include   4.7Mb
    libs      2.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    lib    1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) scriptloc.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Get location of script in a fashion analagous to ${BASH_SOURCE[0]}}
       |                                                          ^
'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.
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                  ^
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                                         ^
checkRd: (-1) geom_flat_violin.Rd:7: Lost braces
     7 | url{https://gist.github.com/dgrtwo/eb7750e74997891d7c20}
       |    ^
checkRd: (-1) sdc_extabs.Rd:59: Lost braces
    59 | (including ]code{forcelist} variables) that can be used to form tables.}
       |                 ^
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
checkRd: (-1) hyperpar.Rd:17: Lost braces
    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R   7.8Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    css_data   8.7Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'secrlinear-vignette.Rmd' using rmarkdown
! Package pdftex.def Error: File `487a948e0c9cf384c922e4ee0a2d77456e2f5507.pdf'
 not found: using draft setting.

Error: processing vignette 'secrlinear-vignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/secrlinear.Rcheck/vign_test/secrlinear/vignettes/secrlinear-vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See secrlinear-vignette.log for more info.
--- failed re-building 'secrlinear-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'secr-datainput.Rmd' using rmarkdown
! Package pdftex.def Error: File `54c84a4252bfb0a62c8c8e15e05f01d9361ab568.png'
 not found: using draft setting.

Error: processing vignette 'secr-datainput.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/secr.Rcheck/vign_test/secr/vignettes/secr-datainput.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See secr-datainput.log for more info.
--- failed re-building 'secr-datainput.Rmd'

--- re-building 'secr-overview.Rmd' using rmarkdown
! Package pdftex.def Error: File `e7e14071003290bed4184f1f3280f57dc9427b53.pdf'
 not found: using draft setting.

Error: processing vignette 'secr-overview.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/secr.Rcheck/vign_test/secr/vignettes/secr-overview.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See secr-overview.log for more info.
--- failed re-building 'secr-overview.Rmd'

SUMMARY: processing the following files failed:
  'secr-datainput.Rmd' 'secr-overview.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'secuTrialR-package-vignette.Rmd' using rmarkdown
! Package pdftex.def Error: File `54bff5ee22cb90594e18be1a842421881f669f79.pdf'
 not found: using draft setting.

Error: processing vignette 'secuTrialR-package-vignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/secuTrialR.Rcheck/vign_test/secuTrialR/vignettes/secuTrialR-package-vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See secuTrialR-package-vignette.log for more info.
--- failed re-building 'secuTrialR-package-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in 'seeclickfixr-Ex.R' failed
The error most likely occurred in:

> ### Name: list_places
> ### Title: Query sub-city neighborhoods in which issues can be reported.
> ### Aliases: list_places
> 
> ### ** Examples
> 
> list_places("Boston, MA",limit = 5)
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html PUBLIC "-//W3C//
                     (right here) ------^
Execution halted
checkRd: (-1) seedCCA.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{u}{numeric, maximum number of projections. The default is 10. This is used for \code{type="seed1"}, \code{type="seed2"} and {tyepe="pls"}.}
       |                                                                                                                                   ^
'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
Error(s) in re-building vignettes:
--- re-building 'MultipleAnalyses.Rmd' using rmarkdown
--- finished re-building 'MultipleAnalyses.Rmd'

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

--- re-building 'SingleStudies.Rmd' using rmarkdown
! Package pdftex.def Error: File `47fa7a5fa41c18374d3ccbd84c92e3e23a41305d.png'
 not found: using draft setting.

Error: processing vignette 'SingleStudies.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/SelfControlledCaseSeries.Rcheck/vign_test/SelfControlledCaseSeries/vignettes/SingleStudies.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SingleStudies.log for more info.
--- failed re-building 'SingleStudies.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    www  34.4Mb
'LazyData' is specified without a 'data' directory
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'semPlot'
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'OpenMx'

Package suggested but not available for checking: 'ctsemOMX'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
checkRd: (-1) sendmail_options.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:38-39: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) match_dataphy.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:39-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:42-44: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs     3.3Mb
    models   1.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'PedComp.Rmd' using rmarkdown
--- finished re-building 'PedComp.Rmd'

--- re-building 'quick_start_example1.rmd' using rmarkdown
--- finished re-building 'quick_start_example1.rmd'

--- re-building 'vignette-age.Rmd' using rmarkdown
! Package pdftex.def Error: File `694b027ef829086ebde6e8d60c7eaca5ba96deb9.pdf'
 not found: using draft setting.

Error: processing vignette 'vignette-age.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/sequoia.Rcheck/vign_test/sequoia/vignettes/vignette-age.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See vignette-age.log for more info.
--- failed re-building 'vignette-age.Rmd'

--- re-building 'vignette-main.Rmd' using rmarkdown
! Package pdftex.def Error: File `ada5a7391433bbe1a2ebdd8ae0463bde6eb13761.pdf'
 not found: using draft setting.

Error: processing vignette 'vignette-main.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/sequoia.Rcheck/vign_test/sequoia/vignettes/vignette-main.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See vignette-main.log for more info.
--- failed re-building 'vignette-main.Rmd'

--- re-building 'flowchart.pdf.asis' using asis
--- finished re-building 'flowchart.pdf.asis'

--- re-building 'vignette_mtDNA.pdf.asis' using asis
--- finished re-building 'vignette_mtDNA.pdf.asis'

SUMMARY: processing the following files failed:
  'vignette-age.Rmd' 'vignette-main.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
GNU make is a SystemRequirements.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   1.3Mb
    libs   3.7Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'FAQs.Rmd' using rmarkdown
--- finished re-building 'FAQs.Rmd'

--- re-building 'Pk_Pv_Pf_Serology_Tutorial.Rmd' using rmarkdown
File ../man/figures/SeroTrackR_Pk_Pf_Pv.jpeg not found in resource path
Error: processing vignette 'Pk_Pv_Pf_Serology_Tutorial.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'Pk_Pv_Pf_Serology_Tutorial.Rmd'

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

--- re-building 'PvSeroApp_R_Tutorial.Rmd' using rmarkdown
File ../man/figures/SeroTrackR_PvSeroApp.jpeg not found in resource path
Error: processing vignette 'PvSeroApp_R_Tutorial.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'PvSeroApp_R_Tutorial.Rmd'

--- re-building 'setup.Rmd' using rmarkdown
File ../man/figures/magpix_raw.jpeg not found in resource path
Error: processing vignette 'setup.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'setup.Rmd'

SUMMARY: processing the following files failed:
  'Pk_Pv_Pf_Serology_Tutorial.Rmd' 'PvSeroApp_R_Tutorial.Rmd'
  'setup.Rmd'

Error: Vignette re-building failed.
Execution halted
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
Package suggested but not available for checking: 'BPCells'
Packages suggested but not available for checking: 'BPCells', 'presto'
Package unavailable to check Rd xrefs: 'BPCells'
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is 123.5Mb
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    gdal     3.0Mb
    libs    94.2Mb
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    sqlite   1.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) bisee.Rd:127: Lost braces
   127 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) hisee.Rd:101: Lost braces
   101 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) isee.Rd:116: Lost braces
   116 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) see.Rd:98: Lost braces
    98 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
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checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                   ^
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) changept.Rd:17-19: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) powerShapeNA.Rd:32-33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    doc    3.1Mb
    libs   1.3Mb
Packages suggested but not available for checking: 'OpenMx', 'rCOSA'
Package unavailable to check Rd xrefs: 'rCOSA'
Package suggested but not available for checking: 'hydromad'
checkRd: (-1) age_corr.Rd:15: Lost braces
    15 | \item{plot}{Should the results be plotted? (/code{TRUE/FALSE})}
       |                                                  ^
checkRd: (-1) age_corr.Rd:17: Lost braces
    17 | \item{agecorrection}{Correct for jumps in age (/code{TRUE}) or
       |                                                     ^
checkRd: (-1) age_corr.Rd:18: Lost braces
    18 | only for starting time (/code{FALSE})}
       |                              ^
installed size is  6.3Mb
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    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiftrPrepare.Rd:37: Lost braces
    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
installed size is  7.7Mb
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Package suggested but not available for checking: 'cmdstanr'
installed size is  9.5Mb
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) js_calls.Rd:63: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) js_calls.Rd:65-66: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) js_calls.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pickCheckboxNamesAndLabels.Rd:14: Lost braces
    14 | \item{choices}{link{pickCheckboxInput} choices list.}
       |                    ^
'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) store_googledrive.Rd:19: Lost braces; missing escapes or markup?
    19 | See the {gargle} package to manage authentication, and especially
       |         ^
checkRd: (-1) store_googledrive.Rd:20: Lost braces; missing escapes or markup?
    20 | \href{https://gargle.r-lib.org/articles/articles/managing-tokens-securely.html}{this vignette from {gargle} package} to manage the process.
       |                                                                                                    ^
checkRd: (-1) custom-labels.Rd:7: Lost braces; missing escapes or markup?
     7 | \title{Modify {shinymanager} labels to use custom text}
       |               ^
checkRd: (-1) use_language.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Use {shinymanager} labels}
       |            ^
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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    shinymgr    1.4Mb
    tutorials   3.6Mb
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
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Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiny_pivot_table.Rd:58: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) shiny_pivot_table.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:64: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
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    R     1.6Mb
    www   6.5Mb
'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: 'cmdstanr'
'LazyData' is specified without a 'data' directory
checkRd: (-1) run_shinytitle_example.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) run_shinytitle_example.Rd:19: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) shutterplot.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.'
       |                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) drr.Rd:36: Lost braces; missing escapes or markup?
    36 |   \code{drr} {is Rosin - Rammler probability density function}\cr
       |              ^
checkRd: (-1) drr.Rd:37: Lost braces; missing escapes or markup?
    37 |   \code{urr} {is Rosin - Rammler cumulative distribution function (CDF) representing undersize mass fraction}\cr
       |              ^
checkRd: (-1) drr.Rd:38: Lost braces
    38 |   \code{orr} {is Rosin - Rammler complementary CDF representing oversize mass fraction ie. relative remainder on the sieve with the mesh size \code{x}}\cr
       |              ^
installed size is  6.1Mb
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    extdata   1.0Mb
    help      1.7Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    extdata   9.8Mb
    libs      1.1Mb
checkRd: (-1) add_k_mer_state.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: 'cmdstanr'
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
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checkRd: (-1) sig.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) sig_report.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
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    64 | \item x_{l,i}, local variable l,
       |         ^
checkRd: (-1) siland.Rd:70: Lost braces; missing escapes or markup?
    70 | \item d_{r,i} the distance between the center of pixel r and the observation at site i.
       |         ^
checkRd: (-1) inlandwaters.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:15: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sim_Y_Binary_X.Rd:51: Lost braces
    51 |     \item \code{dist = "binomial"} is drawn from eqn{Bin(XB, XB(1-XB))}
       |                                                     ^
Error(s) in re-building vignettes:
--- re-building 'sim.BA.Rmd' using rmarkdown
File images/dag.png not found in resource path
Error: processing vignette 'sim.BA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'sim.BA.Rmd'

SUMMARY: processing the following file failed:
  'sim.BA.Rmd'

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

> ### Name: GetApprox
> ### Title: Approximate a copula by a histogram density
> ### Aliases: GetApprox
> 
> ### ** Examples
> 
> Cop <- NewMEVGumbelCopula(3)
> CopApprox <- GetApprox(Cop, dim=2)
> plot(CopApprox)
Error in rgl::rgl.quads(x1, y1, z1, col = rep(sidecol, each = 4), alpha = alpha) : 
  'rgl.quads' is defunct.
Use 'quads3d' instead.
See help("Defunct")
Calls: plot ... plot.CopApprox -> SimCop_binplot_3d -> <Anonymous> -> .Defunct
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
installed size is 15.1Mb
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    extdata  13.0Mb
    libs      1.5Mb
Running 'ex_cvx.R' [88s]
  Running 'fastmerge-ex.R' [7s]
  Running 'smooth.pen_agcv.R' [2s]
Running the tests in 'tests/smooth.pen_agcv.R' failed.
Complete output:
  > library(simest)
  > 
  > ## Test smooth.pen.reg(*, agcv=TRUE) ---------------
  > 
  > ## -- Using a subset of R's sunspots data  ------
  > osV <- abbreviate(gsub("[^[:alnum:]]", '', sub("\\(.*", '', osVersion)), 12)
  > 
  > if(!dev.interactive(TRUE)) pdf(paste0("smooth.pen_sunsp__", osV, ".pdf"), width = 9, height=5)
  > 
  > str(ssp <- window(sunspot.m2014, start = 1900))
  Error: object 'sunspot.m2014' not found
  Execution halted
checkRd: (-1) create_modelDF.Rd:25-38: Lost braces
    25 | convert_xlsx_to_csv<-function(xlsx_file){
       |                                         ^
checkRd: (-1) create_modelDF.Rd:33-36: Lost braces
    33 |   for (i in Sheetnames) {
       |                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) internal.statistics.one.lm.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) internal.statistics.one.lm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) simstudy.logistic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) simstudy.prop2.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'simmer-01-introduction.Rmd' using rmarkdown
--- finished re-building 'simmer-01-introduction.Rmd'

--- re-building 'simmer-02-jss.Rmd' using rmarkdown
! Package pdftex.def Error: File `cad24e9fb24e2c501f964f58cc59922b0e89a98d.pdf'
 not found: using draft setting.

Error: processing vignette 'simmer-02-jss.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/simmer.Rcheck/vign_test/simmer/vignettes/simmer-02-jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See simmer-02-jss.log for more info.
--- failed re-building 'simmer-02-jss.Rmd'

--- re-building 'simmer-03-trajectories.Rmd' using rmarkdown
--- finished re-building 'simmer-03-trajectories.Rmd'

--- re-building 'simmer-04-bank-1.Rmd' using rmarkdown
--- finished re-building 'simmer-04-bank-1.Rmd'

--- re-building 'simmer-04-bank-2.Rmd' using rmarkdown
--- finished re-building 'simmer-04-bank-2.Rmd'

--- re-building 'simmer-05-simpy.Rmd' using rmarkdown
--- finished re-building 'simmer-05-simpy.Rmd'

--- re-building 'simmer-06-queueing.Rmd' using rmarkdown
--- finished re-building 'simmer-06-queueing.Rmd'

--- re-building 'simmer-07-ctmc.Rmd' using rmarkdown
--- finished re-building 'simmer-07-ctmc.Rmd'

--- re-building 'simmer-08-philosophers.Rmd' using rmarkdown
--- finished re-building 'simmer-08-philosophers.Rmd'

--- re-building 'simmer-aa-5G.Rmd' using rmarkdown
--- finished re-building 'simmer-aa-5G.Rmd'

SUMMARY: processing the following file failed:
  'simmer-02-jss.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'OpenMx'
'LazyData' is specified without a 'data' directory
checkRd: (-1) make_one_dataset.Rd:67: Lost braces; missing escapes or markup?
    67 |  \code{within.SD} to be extremely small (e.g., $1 * 10^{-7}$) and all corresponding correlations in matrix
       |                                                        ^
checkRd: (-1) add_bold.Rd:15: Lost braces; missing escapes or markup?
    15 | For example, in latex it would take "2" and output "{\\bf 2}"; in html
       |                                                     ^
installed size is  7.9Mb
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    doc   7.0Mb
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
installed size is 10.1Mb
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    R      2.3Mb
    data   4.8Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) rawCCD.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{distr.type}{school district type (constructed for illustration purposes; (values={"A", "B", "C", "D"})).}
       |                                                                                          ^
checkRd: (-1) selectMatch.Rd:61: Lost braces; missing escapes or markup?
    61 | \item{replacementUnitsFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "replacementUnits.csv"}
       |                                                                    ^
checkRd: (-1) selectMatch.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{subUnitTableFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "subUnitTable.csv"}
       |                                                                ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                  ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                                                                                  ^
'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) ss.cc.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ss.ci.Rd:26: Lost braces
    26 | \item{alpha}{The eqn{\\alpha} error used to compute the \eqn{100*(1-\\alpha)\%} confidence interval}
       |                     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |                 ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                            ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                                        ^
Package which this enhances but not available for checking: 'kmndirs'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
checkRd: (-1) fit_slim.Rd:24: Lost braces; missing escapes or markup?
    24 | sum(x' V^{-1} (y - x beta)) = 0 as the covariance V tends from V[, , 1] +
       |          ^
Error(s) in re-building vignettes:
--- re-building 'slim.Rmd' using rmarkdown
! Package pdftex.def Error: File `f323b61281ac85925289ad2b15b03640aa936786.pdf'
 not found: using draft setting.

Error: processing vignette 'slim.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/slim.Rcheck/vign_test/slim/vignettes/slim.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See slim.log for more info.
--- failed re-building 'slim.Rmd'

SUMMARY: processing the following file failed:
  'slim.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: 'gurobi'
GNU make is a SystemRequirements.
checkRd: (-1) cities_lon_lat.Rd:6: Lost braces
     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Converting_VCF_and_PLINK_formats.Rmd' using rmarkdown
File figure/data_transformation_example_plot-1.png not found in resource path
Error: processing vignette 'Converting_VCF_and_PLINK_formats.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'Converting_VCF_and_PLINK_formats.Rmd'

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

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

SUMMARY: processing the following files failed:
  'Converting_VCF_and_PLINK_formats.Rmd' 'aDNA_smartpca_analysis.Rmd'
  'mallard_smartpca_analysis.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) trlong.Rd:17: Lost braces
    17 |     \item{\code{resp}}{a factor indicating the transport mode choice, and \code{B} denotes taking the bus, code{D} denotes driving one's own vehicle, \code{F} denotes getting a ride with a friend, \code{O} denotes other, and \code{W} denotes walking}
       |                                                                                                                ^
checkRd: (-1) smdocker_log.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:19: Lost braces in \itemize; meant \describe ?
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
GNU make is a SystemRequirements.
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                  ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                            ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                          ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                                    ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                              ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                        ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                      ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                                ^
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) estimMk.Rd:44: Lost braces; missing escapes or markup?
    44 | estimMk returns the transition probability matrix of size (S^{k})xS (with S = length(E)) 
       |                                                              ^
Package suggested but not available for checking: 'doMC'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.5Mb
    libs   1.5Mb
checkRd: (-1) SnakesAndLaddersGame.Rd:25: Lost braces; missing escapes or markup?
    25 | {Hector Haffenden} {haffendenh@cardiff.ac.uk}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                  ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                           ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                                      ^
checkRd: (-1) sk_GLS.Rd:40: Lost braces; missing escapes or markup?
    40 | Operations with V^{-1} are computed using the factorization \code{fac} (see \code{sk_var}), or
       |                   ^
checkRd: (-1) sk_LL.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{quad_form} is z^T V^{-1} z, for the observed response vector z, which is constructed
       |                           ^
checkRd: (-1) sk_var.Rd:41: Lost braces; missing escapes or markup?
    41 | returns the quadratic form X^T V^{-1} X.
       |                                  ^
checkRd: (-1) sk_var.Rd:33: Lost braces; missing escapes or markup?
    33 | either matrix \code{V}, or X^T V^{-1} X, or a factorization ('chol' or 'eigen')
       |                                  ^
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    demo-geotiff   1.3Mb
    doc            3.2Mb
Error(s) in re-building vignettes:
--- re-building 'SNMA_vignette.Rmd' using rmarkdown
! Package pdftex.def Error: File `2bb7cdacb49e3edbd28456a6f5544901b0077e25.pdf'
 not found: using draft setting.

Error: processing vignette 'SNMA_vignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/SNMA.Rcheck/vign_test/SNMA/vignettes/SNMA_vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SNMA_vignette.log for more info.
--- failed re-building 'SNMA_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Found the following significant warnings:
  owen.h:4:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  owen.h:12:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  owen.h:14:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  owen.h:16:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  owen.h:18:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  asa076.h:5:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/snreg.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
Error(s) in re-building vignettes:
--- re-building 'illustration.Rmd' using rmarkdown
File man/figures/doi.png not found in resource path
Error: processing vignette 'illustration.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'illustration.Rmd'

--- re-building 'snreg-vignette.Rmd' using rmarkdown
--- finished re-building 'snreg-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'socialranking.Rmd' using rmarkdown
--- finished re-building 'socialranking.Rmd'

--- re-building 'socialranking_pdf.Rmd' using rmarkdown
! Package pdftex.def Error: File `85bc3488ba39d8955da7d63911308b9d29ee0602.jpg'
 not found: using draft setting.

Error: processing vignette 'socialranking_pdf.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/socialranking.Rcheck/vign_test/socialranking/vignettes/socialranking_pdf.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See socialranking_pdf.log for more info.
--- failed re-building 'socialranking_pdf.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                          ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                        ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                                     ^
checkRd: (-1) s_soda_pred.Rd:8: Lost braces; missing escapes or markup?
     8 | S-SODA assumes within each slice the X vector follow multivariate normal distribution. This function predicts the response y by reverting the P(X | slice(y)) to P(slice(y) | X), and estimates the E(y|X) as sum_{h} E(y | slice(y)=h, X) P (slice(y)=h | X)
       |                                                                                                                                                                                                                   ^
checkRd: (-1) db_compact.Rd:41: Lost braces; missing escapes or markup?
    41 | database structure will be set to true. See GET /{db}. You can also obtain a list of
       |                                                  ^
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     3.2Mb
    doc   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solr_mlt.Rd:70: Lost braces; missing escapes or markup?
    70 | TermVector DEFAULT_FIELD_NAMES = new String[] {"contents"}
       |                                               ^
checkRd: (-1) solve_pH_from_AT.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:93: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
! Package pdftex.def Error: File `1887b37bb7a72ff586790260cf53cbf20bfea159.pdf'
 not found: using draft setting.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/SongEvo.Rcheck/vign_test/SongEvo/vignettes/SongEvo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SongEvo.log for more info.
--- failed re-building 'SongEvo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) load_sorvi_data.Rd:23: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.0Mb
Package suggested but not available for checking: 'gridlayout'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
    libs      1.0Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    include  10.1Mb
    libs      5.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NLMR'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
Package suggested but not available for checking: 'NLMR'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.8Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
    libs      1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sdf_unnest.Rd:20: Lost braces
    20 | \code{a1, a2, a3}, then code{sdf_explode(df, a)} will produce output with each record replicated
       |                             ^
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'SPARRAfairness_example.Rmd' using rmarkdown
[WARNING] Citeproc: citation sparrav4 not found
! Package pdftex.def Error: File `4147f656dc13060a1f8cb4b2c073071902167221.pdf'
 not found: using draft setting.

Error: processing vignette 'SPARRAfairness_example.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/SPARRAfairness.Rcheck/vign_test/SPARRAfairness/vignettes/SPARRAfairness_example.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SPARRAfairness_example.log for more info.
--- failed re-building 'SPARRAfairness_example.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) cholsolveAQinvAT.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Solve the equation X = AQ^{-1}t(A) under permutations}
       |                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |    ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |             ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                      ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                   ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                            ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.sparsereg.Rd:22-23: Lost braces
    22 | \env{main1, main2, main3}{
       |                          ^
checkRd: (-1) plot.sparsereg.Rd:25-27: Lost braces
    25 | \env{xlabel}{
       |             ^
checkRd: (-1) plot.sparsereg.Rd:29-31: Lost braces
    29 | \env{plot.one}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:27-29: Lost braces
    27 | \env{interval}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:31-33: Lost braces
    31 | \env{ci}{
       |         ^
checkRd: (-1) summary.sparsereg.Rd:35-37: Lost braces
    35 | \env{order}{
       |            ^
checkRd: (-1) summary.sparsereg.Rd:39-41: Lost braces
    39 | \env{normal}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:43-45: Lost braces
    43 | \env{select}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:47-48: Lost braces
    47 | \env{printit}{
       |              ^
checkRd: (-1) summary.sparsereg.Rd:50-52: Lost braces
    50 | \env{stage}{
       |            ^
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    help      1.5Mb
Error(s) in re-building vignettes:
--- re-building 'SBSS.Rmd' using rmarkdown
! Package pdftex.def Error: File `2184322edc0f5aa343b96ee87460bf2fffda1e26.pdf'
 not found: using draft setting.

Error: processing vignette 'SBSS.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/SpatialBSS.Rcheck/vign_test/SpatialBSS/vignettes/SBSS.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SBSS.log for more info.
--- failed re-building 'SBSS.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
checkRd: (-1) distSG.Rd:40: Lost braces; missing escapes or markup?
    40 |   matrix and weight matrix (plus a matrix with {eID} identifiers
       |                                                ^
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    help   2.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    help   1.4Mb
    libs   1.0Mb
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', '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.univar',
  '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.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', '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.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', '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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data     2.5Mb
    shapes   3.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    help   1.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
    etc   2.1Mb
checkRd: (-1) findRef.Rd:39: Lost braces
    39 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
checkRd: (-1) hClustAlign.Rd:70: Lost braces
    70 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
checkRd: (-1) FitAkdParameters.Rd:23: Lost braces; missing escapes or markup?
    23 |       p(y|ens) = 1 / K * sum {dnorm(y, z.i, s)} \cr
       |                              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    case   1.8Mb
    libs   2.4Mb
checkRd: (-1) speech_recompiler.Rd:25: Lost braces; missing escapes or markup?
    25 | The default compilation is that of \ code {speech_build (., compiler = TRUE}).
       |                                           ^
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) adaptIntegrateSpherePolar.Rd:14: Lost braces
    14 | code{adaptIntegrateBallPolar()} will likely miss these abrupt changes and give
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) speedtestdata.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:23: Lost braces in \itemize; meant \describe ?
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    doc    1.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs      1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) squidR.Rd:83: Lost braces; missing escapes or markup?
    83 |   \item \code{X1_sto_shared} (default \code{TRUE}): {logical}; if \code{TRUE}, the stochastic environmental effect included in the environmental effect x1 will be shared between individuals. If \code{FALSE}, each individual will experience a different stochastic environmental effect x1 (i.e. a new stochastic environmental effect is generated for each individual).
       |                                                     ^
Running examples in 'srcpkgs-Ex.R' failed
The error most likely occurred in:

> ### Name: pkgs_install
> ### Title: installs a list of source packages
> ### Aliases: pkgs_install
> 
> ### ** Examples
> 
> pkg <- setup_and_get_dummy_srcpkg()
> dest <- tempfile()
> pkgs_install(pkg, dest)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'demo.Rmd' using rmarkdown
--- finished re-building 'demo.Rmd'

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

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

Quitting from testing_and_checking.Rmd:176-179 [checking]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! ! error in pak subprocess
Caused by error in `get_user_cache_dir()`:
! R_USER_CACHE_DIR env var not set during package check, see https://github.com/r-lib/pkgcache#README
---
Backtrace:
     ▆
  1. └─srcpkgs::pkgs_check(small_collection, quiet = TRUE)
  2.   └─srcpkgs::pkgs_install(pkgs, lib, src_pkgs = src_pkgs, quiet = TRUE)
  3.     ├─srcpkgs:::fast_unlist(lapply(pkgs_to_install, .process_pkg))
  4.     │ └─base::unlist(x, recursive, use.names)
  5.     └─base::lapply(pkgs_to_install, .process_pkg)
  6.       └─srcpkgs (local) FUN(X[[i]], ...)
  7.         └─srcpkgs:::pkg_install_nodeps(pkg$path, lib, quiet = quiet, ...)
  8.           ├─withr::with_libpaths(...)
  9.           │ └─base::force(code)
 10.           └─devtools::install(...)
 11.             └─(function() {...
 12.               ├─base::withCallingHandlers(...)
 13.               └─pak::local_install_deps(...)
 14.                 └─pak:::remote(...)
 15.                   └─err$throw(res$error)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'testing_and_checking.Rmd' failed with diagnostics:
! error in pak subprocess
Caused by error in `get_user_cache_dir()`:
! R_USER_CACHE_DIR env var not set during package check, see https://github.com/r-lib/pkgcache#README
--- failed re-building 'testing_and_checking.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) plot.SRCS.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:77-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:87-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:143-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:146-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:149: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) ssaBSS-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
checkRd: (-1) new.distance.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:38-40: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
! Package pdftex.def Error: File `387ca04cc32eb403475d522688c201e41c7b692f.pdf'
 not found: using draft setting.

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/SSN2.Rcheck/vign_test/SSN2/vignettes/introduction.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See introduction.log for more info.
--- 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
checkRd: (-1) SRanalysis.Rd:100: Lost braces
   100 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
checkRd: (-1) StabilizedRegression.Rd:109: Lost braces
   109 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
Error(s) in re-building vignettes:
--- re-building 'stabm.Rmd' using rmarkdown
! Package pdftex.def Error: File `96303ea733e4e88a324023f968ff2d8892584db1.pdf'
 not found: using draft setting.

Error: processing vignette 'stabm.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/stabm.Rcheck/vign_test/stabm/vignettes/stabm.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See stabm.log for more info.
--- failed re-building 'stabm.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) stackExample.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stackExample.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stamppFst.Rd:20: Lost braces
    20 | \code{Fsts}{a matrix of pairwise Fst values between populations}
       |            ^
checkRd: (-1) stamppFst.Rd:21: Lost braces
    21 | \code{Pvalues}{a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix}
       |               ^
checkRd: (-1) stamppFst.Rd:22: Lost braces
    22 | \code{Bootstraps}{a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals}
       |                  ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                                           ^
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    4.4Mb
    help   2.0Mb
installed size is 14.1Mb
  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   5.0Mb
GNU make is a SystemRequirements.
checkRd: (-1) get_fields.Rd:27: Lost braces
    27 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
checkRd: (-1) identify_form_fields.Rd:34: Lost braces
    34 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
checkRd: (-1) stargazer.Rd:229: Lost braces
   229 |   \item{report}{a character string containing only elements of {\code{"v"}, \code{"c"}, \code{"s"},\code{"t"}, \code{"p"}, \code{"*"}} that determines whether, and in which order, variable names (\code{"v"}), coefficients (\code{"c"}), standard errors/confidence intervals (\code{"s"}), test statistics (\code{"t"}) and p-values (\code{"p"}) should be reported in regression tables. If one of the aforementioned letters is followed by an asterisk (\code{"*"}), significance stars will be reported next to the corresponding statistic.}
       |                                                                ^
checkRd: (-1) stargazer.Rd:246: Lost braces
   246 |   \item{table.placement}{a character string containing only elements of {\code{"h"}, \code{"t"},\code{"b"}, \code{"p"}, \code{"!"}, \code{"H"}} that determines the table placement in its LaTeX floating environment.}
       |                                                                         ^
Missing or unexported object: 'CVXR::solve'
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(starnet)
  > 
  > testthat::test_check(package="starnet",stop_on_warning=FALSE)
  Saving _problems/test-92.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 15 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test.R:92:5'): (code run outside of `test_that()`) ──────────────────
  Error: 'solve' is not an exported object from 'namespace:CVXR'
  Backtrace:
      ▆
   1. └─starnet:::.glm(y = list$y, X = list$X, family = family) at test.R:92:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 15 ]
  Error:
  ! Test failures.
  Execution halted
Package suggested but not available for checking: 'starsdata'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    nc    1.7Mb
checkRd: (-1) AutoPollution.Rd:16: Lost braces
    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
! Package pdftex.def Error: File `51bda4e26903c96c8cae2e1a2c3d4cdcff68836a.pdf'
 not found: using draft setting.

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/StateLevelForest.Rcheck/vign_test/StateLevelForest/vignettes/vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See vignette.log for more info.
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   1.3Mb
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'
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    help   1.5Mb
checkRd: (-1) sample2indp.pow.Rd:48: Lost braces
    48 | Pooled standard deviation= \code{sp} = sqrt{((n1 - 1) sigma1^2 +(n2 - 1) sigma2^2) / (n1 + n2 - 2)}
       |                                            ^
checkRd: (-1) tuneParam.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
checkRd: (-1) tuneParamCL2.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) landmarkMatrixToList.Rd:10: Lost braces
    10 |   \item{semilandmark.pattern}{a regular expression pattern passed to \code{sub()} for identifying and grouping curve points. The default is landmark names ending in one or more numbers. To disable grouping, set to code{''}.}
       |                                                                                                                                                                                                                           ^
checkRd: (-1) docker_config_collection.Rd:11: Lost braces; missing escapes or markup?
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("config")}
       | ^
checkRd: (-1) docker_container.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_container")}
       | ^
checkRd: (-1) docker_image_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("image")}
       | ^
checkRd: (-1) docker_plugin_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("plugin")}
       | ^
checkRd: (-1) docker_service_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("service")}
       | ^
checkRd: (-1) docker_task.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_task")}
       | ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    joss_paper   1.2Mb
    libs        12.6Mb
Error(s) in re-building vignettes:
--- re-building 'Alt.Rmd' using rmarkdown
--- finished re-building 'Alt.Rmd'

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

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

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

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

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

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

--- re-building 'kinner.Rmd' using rmarkdown
! Package pdftex.def Error: File `dffe7642ace2b7b3108c0ac981782c4371acb66e.png'
 not found: using draft setting.

Error: processing vignette 'kinner.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/stokes.Rcheck/vign_test/stokes/vignettes/kinner.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See kinner.log for more info.
--- failed re-building 'kinner.Rmd'

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

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
checkRd: (-1) powderymildew.Rd:14-16: Lost braces
    14 | \code{$demographic.coord}{
       |                          ^
checkRd: (-1) powderymildew.Rd:18-20: Lost braces
    18 | \code{$genetic.coord}{
       |                      ^
checkRd: (-1) powderymildew.Rd:22-24: Lost braces
    22 | \code{$demographic.measures}{
       |                             ^
checkRd: (-1) powderymildew.Rd:26-28: Lost braces
    26 | \code{$genetic.frequencies}{
       |                            ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'StrathE2E2examples'
checkRd: (-1) StrathE2E2-package.Rd:70: Lost braces; missing escapes or markup?
    70 | {Basic model operations:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:79: Lost braces; missing escapes or markup?
    79 | {Parameter estimation:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:88: Lost braces; missing escapes or markup?
    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:98: Lost braces; missing escapes or markup?
    98 | {Compare model runs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:105: Lost braces; missing escapes or markup?
   105 | {Fishery yield analysis:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:111: Lost braces; missing escapes or markup?
   111 | {Visualize model inputs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:117: Lost braces; missing escapes or markup?
   117 | {Visualize model outputs:} \cr
       | ^
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installed size is 11.3Mb
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    libs  10.6Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 35.4Mb
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    libs  34.5Mb
installed size is  9.1Mb
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    doc    7.2Mb
    libs   1.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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    doc       2.0Mb
    extdata   2.9Mb
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
Found the following significant warnings:
  functions.c:46:39: warning: ISO C forbids empty initializer braces before C2X [-Wpedantic]
  functions.c:51:28: warning: ISO C forbids empty initializer braces before C2X [-Wpedantic]
  functions.c:107:33: warning: ISO C forbids empty initializer braces before C2X [-Wpedantic]
  functions.c:108:33: warning: ISO C forbids empty initializer braces before C2X [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.4/structenforcement.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                        ^
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                            ^
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                        ^
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                            ^
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    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
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Package suggested but not available for checking: 'MOFAdata'
installed size is  9.6Mb
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    30 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{csvdata}
       |                                ^
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    88 | \item{jsondata}{\code{deprecated} use data argument instead; data in nested d3 JSON hierarchy with `{name:...,  children:[];}`}
       |                                                                                                     ^
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    22 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{list}, \code{character},
       |                                ^
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    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
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checkRd: (-1) getFittedProbs.Rd:6-8: Lost braces
     6 | getFittedValues <- function(object) {
       |                                     ^
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    14 | getFittedValues <- function(object) {
       |                                     ^
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Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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GNU make is a SystemRequirements.
installed size is  7.2Mb
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GNU make is a SystemRequirements.
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    76 | The estimation procedure here is performed using coxph {survival} and inserting these estimated
       |                                                        ^
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    24 | set, svKomodo loads {svSocket}, starts the socket server listening to the
       |                     ^
checkRd: (-1) svKomodo-package.Rd:18: Lost braces; missing escapes or markup?
    18 | Komodo and (2) the present {svKomodo} R package that work hand in hand to
       |                            ^
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    28 | Nevertheless, the SciViews-K Komodo addin and the {svKomodo} R package
       |                                                   ^
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    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                          ^
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    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                                         ^
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    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
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    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
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Packages required but not available: 'OpenMx', 'metaSEM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
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installed size is  6.7Mb
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installed size is  5.6Mb
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installed size is  9.4Mb
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    68 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    67 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
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   119 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
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    59 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/TaxaNorm.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'lyrics.Rmd' using rmarkdown
--- finished re-building 'lyrics.Rmd'

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

Quitting from palettes.Rmd:91-104 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! object 'penguins' not found
---
Backtrace:
    ▆
 1. └─ggplot2::ggplot(penguins, aes(x = bill_len, y = bill_dep))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Quitting from plotting.Rmd:65-70 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! object 'penguins' not found
---
Backtrace:
    ▆
 1. └─ggplot2::ggplot(penguins, aes(x = bill_len, y = bill_dep))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

SUMMARY: processing the following files failed:
  'palettes.Rmd' 'plotting.Rmd'

Error: Vignette re-building failed.
Execution halted
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    35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^
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    libs   1.1Mb
GNU make is a SystemRequirements.
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    help   2.8Mb
installed size is 113.7Mb
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    libs  97.5Mb
    proj   9.0Mb
installed size is 23.3Mb
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Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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    37 |  {The 2 in the first row means there are two cycles;}
       |  ^
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    38 |   {The second row means there is a cycle of length 2, with members  (1,3);}
       |   ^
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    39 |  {The third row means  there is a cycle of length 1, with member  (2);}
       |  ^
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    40 |  {The fourth row is redundant for this specific case.}
       |  ^
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    41 |  {One can read from the output of permucycle() to obtain cycle notation (13)(2) of the permutation, and other information.}
       |  ^
Package which this enhances but not available for checking: 'metaSEM'
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    16 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variatioanl approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
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    26 | It is recommended to use link{sibp_param_search} instead of this function to search over multiple configurations of the most important parameters.  So long as only the training data is used, the analyst can freely experimient with as many parameter configurations as he likes without corrupting his causal inferences.  Once a parameter configuration is chosen, the user can then use \link{sibp_amce} on the test set to estimate the average marginal component effect (AMCE) for each treatment.}
       |                              ^
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    28 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variational approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
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    19 |   \item{sibp.amce}{The table returned by code{sibp_amce}.}
       |                                              ^
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    20 |  \\tabular{rrrrr}{
       |           ^
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    20 |  \\tabular{rrrrr}{
       |                  ^
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Error(s) in re-building vignettes:
--- re-building 'v01_intro.Rmd' using rmarkdown
File "man/figures/korea_map.png" not found in resource path
Error: processing vignette 'v01_intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'v01_intro.Rmd'

--- re-building 'v02_regional_analysis.Rmd' using rmarkdown
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--- re-building 'v04_data_cleaning_kosis.Rmd' using rmarkdown
--- finished re-building 'v04_data_cleaning_kosis.Rmd'

--- re-building 'v05_contributors_guide.Rmd' using rmarkdown
--- finished re-building 'v05_contributors_guide.Rmd'

SUMMARY: processing the following file failed:
  'v01_intro.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Package suggested but not available for checking: 'OpenMx'
Package suggested but not available for checking: 'admixtools'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.1Mb
    libs      1.6Mb
Error(s) in re-building vignettes:
--- re-building 'creating_prompt_wraps.Rmd' using rmarkdown
--- finished re-building 'creating_prompt_wraps.Rmd'

--- re-building 'getting_started.Rmd' using rmarkdown
File ../man/figures/answer_using_r1-1.png not found in resource path
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'getting_started.Rmd'

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

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

SUMMARY: processing the following files failed:
  'getting_started.Rmd' 'sentiment_analysis.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    2.2Mb
Packages suggested but not available for checking: 'umx', 'OpenMx'
installed size is  6.2Mb
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    doc   5.4Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Tigger-Vignette.Rmd' using rmarkdown
! Package pdftex.def Error: File `7c69f819751f61ac689dde7f6d6cc262e77b3743.pdf'
 not found: using draft setting.

Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/tigger.Rcheck/vign_test/tigger/vignettes/Tigger-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Tigger-Vignette.log for more info.
--- failed re-building 'Tigger-Vignette.Rmd'

SUMMARY: processing the following file failed:
  'Tigger-Vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'rrelaxiv'
installed size is 26.1Mb
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    libs    22.2Mb
    tiledb   1.4Mb
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) alcohol.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:22-26: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    help   1.1Mb
    libs   4.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) partition_undirected_graph.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{cutoff}{Numeric. The value max(0, g_{i,j} - cutoff) so that there are <\code{.num_components}> components in the graph.}
       |                                           ^
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
checkRd: (-1) tierChart.Rd:332: Lost braces
   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
Error(s) in re-building vignettes:
--- re-building 'titan2-intro.Rmd' using rmarkdown
! Unable to load picture or PDF file 'e103fbb4d43d274105d601d74ed3b0a46d5b16c8.
pdf'.
<to be read again> 
                   }
l.670 ...fbb4d43d274105d601d74ed3b0a46d5b16c8.pdf}

Error: processing vignette 'titan2-intro.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/TITAN2.Rcheck/vign_test/TITAN2/vignettes/titan2-intro.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See titan2-intro.log for more info.
--- failed re-building 'titan2-intro.Rmd'

SUMMARY: processing the following file failed:
  'titan2-intro.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 'titrationCurves.Rmd' using rmarkdown
! Package pdftex.def Error: File `e22099aa82b01303e1ec9b1bc833db5944645b57.pdf'
 not found: using draft setting.

Error: processing vignette 'titrationCurves.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/titrationCurves.Rcheck/vign_test/titrationCurves/vignettes/titrationCurves.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See titrationCurves.log for more info.
--- failed re-building 'titrationCurves.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) pmvn.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) tv_episode_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the episode_id value found in the change entries.
       |                                                 ^
checkRd: (-1) tv_season_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the season_id value found in the change entries.
       |                                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pvalEffectPlot.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:94: Lost braces in \itemize; meant \describe ?
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) jsonStr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
checkRd: (-1) jsonStr.Rd:18: Lost braces; missing escapes or markup?
    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
checkRd: (-1) fixed_width_no_modeling.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
Error(s) in re-building vignettes:
--- re-building 'toolStability.Rmd' using rmarkdown
! Package pdftex.def Error: File `7d15159c30a9419d63fe08439e25f4219c26ad7c.pdf'
 not found: using draft setting.

Error: processing vignette 'toolStability.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/toolStability.Rcheck/vign_test/toolStability/vignettes/toolStability.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See toolStability.log for more info.
--- failed re-building 'toolStability.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^
checkRd: (-1) getSegsExtra.Rd:14: Lost braces
    14 | \item{data}{data.table returned from function /code{tdtr}}
       |                                                    ^
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: 'gurobi'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    R         5.9Mb
    help      1.8Mb
    include   1.9Mb
    libs      9.3Mb
Package suggested but not available for checking: 'toscaData'
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'utils'
A package should be listed in only one of these fields.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc  12.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    2.6Mb
checkRd: (-1) trait_missing.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: 'taxidata'
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  13.3Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fwelnet', 'doMC'
Missing or unexported objects:
  'CVXR::diff' 'CVXR::solve'
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(transreg)
  > 
  > testthat::test_check(package="transreg",stop_on_warning=FALSE)
  Saving _problems/test-26.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test.R:26:3'): (code run outside of `test_that()`) ──────────────────
  Error: 'diff' is not an exported object from 'namespace:CVXR'
  Backtrace:
      ▆
   1. └─transreg:::.iso.slow.single(...) at test.R:26:3
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
checkRd: (-1) trtsel.Rd:69: Lost braces; missing escapes or markup?
    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
Package suggested but not available for checking: 'TreeDistData'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
install log '' does not exist
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.2Mb
    doc       1.3Mb
    extdata  14.8Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'TriMatch.Rmd' using rmarkdown
! Package pdftex.def Error: File `9128373b2567ab3b0615a8a777527fee17d665e4.pdf'
 not found: using draft setting.

Error: processing vignette 'TriMatch.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/TriMatch.Rcheck/vign_test/TriMatch/vignettes/TriMatch.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See TriMatch.log for more info.
--- failed re-building 'TriMatch.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) summary.armasubsets.Rd:16: Lost braces
    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
checkRd: (-1) tsBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:34: Lost braces in \itemize; meant \describe ?
'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: \&
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) repr_dwt.Rd:28: Lost braces; missing escapes or markup?
    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
'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
checkRd: (-1) twosigmag.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
Package which this enhances but not available for checking: 'sl3'
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'neun_euro_ticket_demonstrator.Rmd' using rmarkdown
--- finished re-building 'neun_euro_ticket_demonstrator.Rmd'

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

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc     4.5Mb
    ubinc   2.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.1Mb
    libs   4.3Mb
GNU make is a SystemRequirements.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    shinyapp   5.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    dummydata   1.4Mb
    libs        2.5Mb
Package suggested but not available for checking: 'MBESS'
'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: 'OpenMx'

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
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
checkRd: (-1) reg_1d.Rd:42: Lost braces; missing escapes or markup?
    42 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
checkRd: (-1) reg_2d.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) simRedCard.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simRedCard.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.4Mb
    libs  14.9Mb
GNU make is a SystemRequirements.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'USAboundariesData'
Package suggested but not available for checking: 'USA.state.boundaries.data'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  22.5Mb
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
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Error(s) in re-building vignettes:
--- re-building 'VALERIE.Rmd' using rmarkdown
! Package pdftex.def Error: File `ae1f81e7f5d6239e8c4e5d45bf832245c4cad9ee.pdf'
 not found: using draft setting.

Error: processing vignette 'VALERIE.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/VALERIE.Rcheck/vign_test/VALERIE/vignettes/VALERIE.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See VALERIE.log for more info.
--- failed re-building 'VALERIE.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) sendTasks.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sendTasks.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
installed size is 109.3Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    gdal      3.0Mb
    libs     93.2Mb
    proj      9.0Mb
checkRd: (-1) sample_gen.Rd:18: Lost braces; missing escapes or markup?
    18 | Generate \code{n} random samples from multivariate Gaussian distribution N(0, (L^TL)^{-1})
       |                                                                                      ^
'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) vardannual.Rd:97: Lost braces
    97 | \item{ID_level2}{Optional}{variable for unit ID codes. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                           ^
checkRd: (-1) vardannual.Rd:99: Lost braces
    99 | \item{dataset}{Optional}{survey data object convertible to \code{data.table}.}
       |                         ^
checkRd: (-1) vardcrospoor.Rd:122: Lost braces
   122 | \item{ind_gr}{Optional}{variable by which divided independently X matrix of the auxiliary variables for the calibration. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                        ^
checkRd: (-1) vardcrospoor.Rd:124: Lost braces
   124 | \item{use.estVar}{Logical}{value. If value is \code{TRUE}, then \code{R} function \code{estVar} is used for the  estimation of covariance matrix of the residuals. If value is \code{FALSE}, then \code{R} function \code{estVar} is not used for the estimation of covariance matrix of the residuals.}
       |                           ^
checkRd: (-1) vardom_othstr.Rd:69: Lost braces
    69 | \item{percentratio}{Positive}{numeric value. All linearized variables are multiplied with \code{percentratio} value, by default - 1.}
       |                              ^
checkRd: (-1) varpoord.Rd:121: Lost braces
   121 | \item{month_at_work}{Variable}{for total number of month at work (sum of the number of months spent at full-time work as employee, number of months spent at part-time work as employee, number of months spent at full-time work as self-employed (including family worker), number of months spent at part-time work as self-employed (including family worker)).  One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                               ^
'LazyData' is specified without a 'data' directory
Running examples in 'vardpoor-Ex.R' failed
The error most likely occurred in:

> ### Name: vardannual
> ### Title: Variance estimation for measures of annual net change or annual
> ###   for single and multistage stage cluster sampling designs
> ### Aliases: vardannual
> ### Keywords: vardannual
> 
> ### ** Examples
> 
>  
> ### Example
> library("data.table")
> 
> set.seed(1)
> 
> data("eusilc", package = "laeken")
> eusilc1 <- eusilc[1:20, ]
> rm(eusilc)
> 
> dataset1 <- data.table(rbind(eusilc1, eusilc1),
+                        year = c(rep(2010, nrow(eusilc1)),
+                                 rep(2011, nrow(eusilc1))))
> rm(eusilc1)
> 
> dataset1[, country := "AT"]
> dataset1[, half := .I - 2 * trunc((.I - 1) / 2)]
> dataset1[, quarter := .I - 4 * trunc((.I - 1) / 4)]
> dataset1[age < 0, age := 0]
> 
> PSU <- dataset1[, .N, keyby = "db030"][, N := NULL][]
> PSU[, PSU := trunc(runif(.N, 0, 5))]
> 
> dataset1 <- merge(dataset1, PSU, all = TRUE, by = "db030")
> rm(PSU)
> 
> dataset1[, strata := "XXXX"]
> dataset1[, employed := trunc(runif(.N, 0, 2))]
> dataset1[, unemployed := trunc(runif(.N, 0, 2))]
> dataset1[, labour_force := employed + unemployed]
> dataset1[, id_lv2 := paste0("V", .I)]
> 
> vardannual(Y = "employed", H = "strata",
+            PSU = "PSU", w_final = "rb050",
+            ID_level1 = "db030", ID_level2 = "id_lv2",
+            Dom = NULL, Z = NULL, years = "year",
+            subperiods = "half", dataset = dataset1,
+            percentratio = 100, confidence = 0.95,
+            method = "cros")
Error in t(X) %*% A_matrix : non-conformable arguments
Calls: vardannual -> lapply -> FUN -> data.table
Execution halted
checkRd: (-1) betaburr.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Burr distribution due to Parana\'{i}ba et al. (2011) given by
       |                                                                                                                        ^
checkRd: (-1) betafrechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Fr\'{e}chet distribution due to Barreto-Souza et al. (2011) given by
       |                                                                                           ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                      ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                                                      ^
checkRd: (-1) kumburr7.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Kumaraswamy Burr XII distribution due to Parana\'{i}ba et al. (2013) given by
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateDCSIS.Rd:40: Lost braces
    40 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + exp(2*X22)*e
       |                                ^
checkRd: (-1) simulateDCSIS.Rd:42: Lost braces
    42 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + 6*X22 + e
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get.miniseq.sample.files.Rd:15: Lost braces
    15 | \item{file.suffix}{Regex expression for end of file name. For example, `file.suffix = '_S\\d{1,2}_.*_R1_.*'` will match R1 files.1 files.}
       |                                                                                             ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) decomposition.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
checkRd: (-1) moving.estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) additiveBeta.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:41: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) additiveBeta.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:27: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) downloadPBDB.Rd:33: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) multiplicativeBeta.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without 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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installed size is  8.4Mb
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    R      4.3Mb
    help   3.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) VirtualArray-single-bracket-method.Rd:6: Lost braces
     6 | \title{Indexing to extract subsets of a 'code{\link[via:XArray-class]{VirtualArray}}'-class object}
       |                                              ^
checkRd: (-1) subset.Rd:20: Lost braces
    20 | \item{drop}{\code{logical} in case the result of subsetting is a single element, should the \\code{\link[via:XArray-class]{VirtualArray}} wrapper be dropped?}
       |                                                                                                   ^
installed size is 10.8Mb
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checkRd: (-1) vic_param.Rd:311: Lost braces
   311 | albedo must be supplied in code{forcing_veg}. Default = 1.}
       |                                ^
checkRd: (-1) vic_param.Rd:323: Lost braces
   323 | supplied in code{forcing_veg}. Default = 1.}
       |                 ^
checkRd: (-1) vic_param.Rd:341: Lost braces
   341 | be supplied in code{forcing_veg} Default = 0.}
       |                    ^
checkRd: (-1) vietnamcode.Rd:28: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) vietnamcode_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:16: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) compdesc.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) compdesc.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
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    htmlwidgets   6.8Mb
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    libs   1.2Mb
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checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
installed size is 24.0Mb
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GNU make is a SystemRequirements.
installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) Data-Examples.Rd:39: Lost braces in \itemize; meant \describe ?
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Error(s) in re-building vignettes:
--- re-building 'VsusPVignette.Rmd' using rmarkdown
! Package pdftex.def Error: File `a90c02d95f01b9993af80cfee09fab1d4e74c879.pdf'
 not found: using draft setting.

Error: processing vignette 'VsusPVignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/VsusP.Rcheck/vign_test/VsusP/vignettes/VsusPVignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See VsusPVignette.log for more info.
--- failed re-building 'VsusPVignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) WACS.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:20: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) WACS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACSreadAgroclim.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) WACSreadAgroclim.Rd:16-17: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
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installed size is 28.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'examples.Rmd' using rmarkdown
! Package pdftex.def Error: File `961847769b84fd3cb67432c5344a2ce49363cdfc.pdf'
 not found: using draft setting.

Error: processing vignette 'examples.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/waydown.Rcheck/vign_test/waydown/vignettes/examples.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See examples.log for more info.
--- 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
Error(s) in re-building vignettes:
--- re-building 'wCorrArguments.Rmd' using rmarkdown
! Package pdftex.def Error: File `45ccd6ee812f80ef9e9586abfbf6d6659297b23b.pdf'
 not found: using draft setting.

Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrArguments.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrArguments.log for more info.
--- failed re-building 'wCorrArguments.Rmd'

--- re-building 'wCorrFormulas.Rmd' using rmarkdown
! Package pdftex.def Error: File `8257131a94bf62ecbb5b6740ba75ea5bf05d84c1.pdf'
 not found: using draft setting.

Error: processing vignette 'wCorrFormulas.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrFormulas.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrFormulas.log for more info.
--- failed re-building 'wCorrFormulas.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'wcvpdata'
Package suggested but not available for checking: 'prepr'
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    libs   7.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) busTrace.Rd:15: Lost braces
    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
checkRd: (-1) WeightedROC.Rd:10: Lost braces; missing escapes or markup?
    10 | integer/numeric with values all in {0=negative,1=positive} or
       |                                    ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       | ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       |                            ^
checkRd: (-1) CLIC.Rd:149: Lost braces
   149 | Composite likelihood {E}{M} algorithm with applications to
       |                         ^
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Running 'testthat.R' [408s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(whirl)
  > 
  > test_check("whirl")
  Saving _problems/test-mdformats-35.R
  
                              
  [ FAIL 1 | WARN 0 | SKIP 16 | PASS 150 ]
  
  ══ Skipped tests (16) ══════════════════════════════════════════════════════════
  • On CRAN (16): 'test-biocompute.R:1:1', 'test-custom_logging.R:19:1',
    'test-examples.R:2:3', 'test-python.R:2:3', 'test-python.R:44:3',
    'test-run.R:33:3', 'test-run.R:76:3', 'test-run.R:87:3', 'test-run.R:95:3',
    'test-run.R:112:3', 'test-run.R:134:3', 'test-run.R:151:3',
    'test-run.R:161:3', 'test-strace.R:42:3', 'test-util_queue_summary.R:11:3',
    'test-whirl_queue.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-mdformats.R:29:3'): pandoc works ─────────────────────────────
  Expected `all(...)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 1 | WARN 0 | SKIP 16 | PASS 150 ]
  Error:
  ! Test failures.
  Execution halted
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GNU make is a SystemRequirements.
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checkRd: (-1) milakes.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:22: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  stop.c:10:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/winch.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
checkRd: (-1) secondDerivative.Rd:14: Lost braces
    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
checkRd: (-1) windAC.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:33: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
--- re-building 'wlsd.Rmd' using rmarkdown
Error reading bibliography file wlsd.bib:
(line 70, column 31):
unexpected '%'
expecting white space
Error: processing vignette 'wlsd.Rmd' failed with diagnostics:
pandoc document conversion failed with error 25
--- failed re-building 'wlsd.Rmd'

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

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

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

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'wsynvignette.Rmd' using rmarkdown
! Package pdftex.def Error: File `007a544c05152bc1218bdda8d55422f5318da222.pdf'
 not found: using draft setting.

Error: processing vignette 'wsynvignette.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/wsyn.Rcheck/vign_test/wsyn/vignettes/wsynvignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wsynvignette.log for more info.
--- failed re-building 'wsynvignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) wtest.Rd:61-64: Lost braces
    61 | {When \code{w.order} =2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) wtest.high.Rd:61-64: Lost braces
    61 | {When \code{w.order} > 2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) exploreSignatures.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:67-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateData.Rd:47: Lost braces
    47 | \bold{code{data}} \tab the generated data \cr
       |           ^
checkRd: (-1) generateData.Rd:53: Lost braces
    53 | Refer to \bold{\emph{code{\link{retrieveDataFactory}}}} and to
       |                          ^
checkRd: (-1) qualifyFunctionArguments.Rd:14: Lost braces
    14 | A emph{\code{list}} with following names
       |       ^
checkRd: (-1) qualifyFunctionArguments.Rd:26: Lost braces
    26 | \item{code{arguments}}{a \code{pairList} of argument names and values.
       |           ^
checkRd: (-1) completeManualPage.Rd:12: Lost braces
    12 | See \emph{\bold{code{\link{ProcessingContext}}}}. Only
       |                     ^
checkRd: (-1) produceAllManualPagesFromObject.Rd:14: Lost braces
    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
checkRd: (-1) chemnet.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chemnet.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:105: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    java  26.7Mb
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    java  11.7Mb
checkRd: (-1) xml_to_df.Rd:144: Lost braces; missing escapes or markup?
   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: namespace 'nlmixr2est' is not available and has been replaced
  Warning: namespace 'rxode2' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/4.4/xpose.xtras.Rcheck/00install.out' for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    3.2Mb
Running examples in 'xpose.xtras-Ex.R' failed
The error most likely occurred in:

> ### Name: backfill_nlmixr2_props
> ### Title: Populate some properties from nlmixr2 fit
> ### Aliases: backfill_nlmixr2_props
> 
> ### ** Examples
> 
> 
> xpdb_nlmixr2 %>%
+   set_prop(condn = "not implemented") %>%
+   get_prop("condn")
[1] "not implemented"
> 
> xpdb_nlmixr2 %>%
+   set_prop(condn = "not implemented") %>%
+   backfill_nlmixr2_props() %>%
+   get_prop("condn")
Error in `backfill_nlmixr2_props()`:
! Incompatible nlmixr2/rxode2 fit object detected
ℹ This object was created with rxode2 < 5.0 and cannot be used with rxode2 >= 5.0
✖ The internal rxUi structure is incompatible between versions
! Please regenerate the fit object using current versions of nlmixr2est and rxode2
Backtrace:
    ▆
 1. ├─... %>% get_prop("condn")
 2. ├─xpose.xtras::get_prop(., "condn")
 3. │ └─xpose::get_summary(xpdb)
 4. │   └─xpose::check_xpdb(xpdb, check = "summary")
 5. │     └─xpose::is.xpdb(xpdb)
 6. └─xpose.xtras::backfill_nlmixr2_props(.)
 7.   └─rlang::abort(...)
Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [342s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(xpose.xtras)
  ℹ xpose is not currently attached.
  
  Attaching package: 'xpose.xtras'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("xpose.xtras")
  Saving _problems/test-nlmixr2-10.R
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 847 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-covariates.R:123:3', 'test-xplot_boxplot.R:157:3',
    'test-xplot_pairs.R:44:3', 'test-xset_features.R:170:3',
    'test-xset_features.R:170:3', 'test-xset_features.R:170:3',
    'test-xset_features.R:170:3'
  • requireNamespace("rxode2", quietly = TRUE) && "rxDerived" %in%
    getNamespaceExports("rxode2") is TRUE (2): 'test-diag_constants.R:123:3',
    'test-diag_constants.R:129:3'
  • {qs} is not installed (1): 'test-nlmixr2.R:317:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-nlmixr2.R:8:3'): old fit detection works correctly ───────────
  Expected `test_nlmixr2_is_old_fit(xpdb_nlmixr2)` to be FALSE.
  Differences:
  `actual`:   TRUE 
  `expected`: FALSE
  
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 847 ]
  Error:
  ! Test failures.
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) xwfGridsearch.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{iter}{Number of levels in the adaptive grid search. The resolution in b obtained is 2^{-1-iter}.}
       |                                                                                             ^
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.1Mb
Package suggested but not available for checking: 'MBESS'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) glm.cons.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{method}{the method used in fitting the model. The default method "\code{glm.fit.cons}" uses function {nnnpls} from package nnls instead of \code{lm.fit} to impose the sign of the coefficients. As in \code{glm}, the alternative method "\code{model.frame}" returns the model frame and does no fitting.}
       |                                                                                                            ^
Running examples in 'zetadiv-Ex.R' failed
The error most likely occurred in:

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

$combinations
[1] 302621

$zeta.val
[1] 57.61204

$zeta.val.sd
[1] 13.10351

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