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    75 |   \item \strong{Pollen productivity}: In each time step the model computes the pollen productivity (in relative values) of the population using the equation \eqn{P_{t} = \sum x_{it} \times max(S_{t}, B)}, where \emph{t} is time (a given simulation time step), \emph{P} is the pollen productivity of the population at a given time, \emph{x_{i}} represents the biomass of every adult individual, \emph{S} is the environmental suitability at the given time, \emph{B} is the contribution of biomass to pollen productivity regardless of environmental suitability (\emph{pollen.control} parameter in the simulation, 0 by default). If \emph{B} equals 1, \emph{P} is equal to the total biomass sum of the adult population, regardless of the environmental suitability. If \emph{B} equals 0, pollen productivity depends entirely on environmental suitability values.
       |                                                                                                                                                                                                                                                                                                                                                    ^
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    16 |   ...{currently not used}
       |      ^
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    32 | A call to {new} returns a newly allocated object from the class identified by the first argument.
       |           ^
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    37 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the amino acids at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
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    36 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the nucleotides at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
Specified C++11: please drop specification unless essential
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    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
installed size is 23.8Mb
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    libs     21.9Mb
GNU make is a SystemRequirements.
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Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
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     9 | Zeeden et al., (2013) and anchored to the code{\link{astrosignal_example}} \cr
       |                                               ^
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   206 | be off in certain intervals. the link[WaverideR]{retrack_wt_MC} mitigates
       |                                                 ^
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    40 | link[WaverideR]{analyze_wavelet} wavelet function
       |                ^
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    41 | To create a list use the link[base]{list} function}
       |                                    ^
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    44 | To create the matrix use the link[base]{cbind} function and only add the
       |                                        ^
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    58 | <structure search> is assembled as "{\code{substructure} |
       |                                     ^
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    59 | \code{superstructure} | \code{similarity} | \code{identity}} / {\code{smiles}
       |                                                                ^
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    70 | "{\code{fastidentity} | \code{fastsimilarity_2d} | \code{fastsimilarity_3d} |
       |  ^
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    71 | \code{fastsubstructure} | \code{fastsuperstructure}}/{\code{smiles} |
       |                                                      ^
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   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
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GNU make is a SystemRequirements.
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    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
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    10 | integer/numeric with values all in {0=negative,1=positive} or
       |                                    ^
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    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       | ^
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    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       |                            ^
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   149 | Composite likelihood {E}{M} algorithm with applications to
       |                         ^
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    Major changes
    Minor changes
installed size is  8.5Mb
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    data   4.2Mb
    libs   3.7Mb
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    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
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    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
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    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
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    32 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
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    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.
       | ^
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    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.
       | ^
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    47 | \bold{code{data}} \tab the generated data \cr
       |           ^
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    53 | Refer to \bold{\emph{code{\link{retrieveDataFactory}}}} and to
       |                          ^
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    14 | A emph{\code{list}} with following names
       |       ^
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    26 | \item{code{arguments}}{a \code{pairList} of argument names and values.
       |           ^
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    12 | See \emph{\bold{code{\link{ProcessingContext}}}}. Only
       |                     ^
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    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
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  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    java  26.1Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
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
Found the following significant warnings:
  DocParse.c:1334:5: warning: 'xmlKeepBlanksDefault' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:134:7: warning: 'xmlSkipBlankChars' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:135:7: warning: 'xmlParseMarkupDecl' is deprecated [-Wdeprecated-declarations]
  RUtils.c:142:5: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.4/XML.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.4Mb
'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}.}
       |                                                                                             ^
checkRd: (-1) cat_sim.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{min} and {max} are mandatory for setting limits on the test length. User-defined
       |                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) boot.yhat.Rd:3: Lost braces
     3 | \title{Bootstrap metrics produced from /code{calc.yhat}}
       |                                             ^
checkRd: (-1) boot.yhat.Rd:19: Lost braces
    19 |     Ouput of /code{lm}
       |                   ^
checkRd: (-1) boot.yhat.Rd:22: Lost braces
    22 |     Output of /code{calc.yhat}
       |                    ^
checkRd: (-1) booteval.yhat.rd:3: Lost braces
     3 | \title{Evaluate bootstrap metrics produced from /code{calc.yhat}}
       |                                                      ^
checkRd: (-1) booteval.yhat.rd:5: Lost braces
     5 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) combCI.rd:26: Lost braces
    26 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) commonality.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) dombin.rd:12: Lost braces
    12 |     Output from /code{dominance}
       |                      ^
checkRd: (-1) dominance.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) plotCI.yhat.rd:5: Lost braces
     5 |   This function plots CIs that have been produced from /code{booteval.yhat}.
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:32: Lost braces
    32 |   This function plots CIs that have been produced from /code{booteval.yhat}.   
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:35: Lost braces
    35 | This returns a plot of CIs that have been produced from /code{booteval.yhat}.
       |                                                              ^
'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.}
       |                                                                                                            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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"}.
       |                                          ^
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  30.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 105.5Mb
  sub-directories of 1Mb or more:
    libs  104.5Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   2.9Mb
    libs      8.2Mb
'LazyData' is specified without a 'data' directory
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    include  13.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R  14.1Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'DeconRNASeq', 'WGCNA'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
'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  9.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   3.0Mb
    libs   2.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    data    1.3Mb
    files   1.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.7Mb
installed size is 151.9Mb
  sub-directories of 1Mb or more:
    adelie    1.2Mb
    libs    149.6Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data  10.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Packages suggested but not available for checking: 'HiTC', 'snpStats'
Package unavailable to check Rd xrefs: ‘snpStats’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lintr’ ‘pharmaversesdtm’ ‘pkgdown’ ‘testthat’
A package should be listed in only one of these fields.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package which this enhances but not available for checking: ‘asreml’
Specified C++11: please drop specification unless essential
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  30.7Mb
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
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checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
'LazyData' is specified without a 'data' directory
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checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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installed size is 32.9Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    31.4Mb
'LazyData' is specified without a 'data' directory
Bad \usage lines found in documentation object 'annmatrix':
  <unescaped bksl>method{@}{annmatrix}(object, name)
  <unescaped bksl>method{@}{annmatrix}(object, name) <- value

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘GEOquery’
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    R  36.1Mb
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
'LazyData' is specified without a 'data' directory
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.2Mb
    libs   1.6Mb
Specified C++11: please drop specification unless essential
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    documents     2.4Mb
    libs          5.5Mb
    screenshots   1.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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    extdata   5.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.1Mb
    doc    1.8Mb
sort_asap: no visible global function definition for ‘sort_by’
Undefined global functions or variables:
  sort_by
Package suggested but not available for checking: ‘arcgisbinding’
Package suggested but not available for checking: ‘ArchaeoData’
Found the following significant warnings:
  Warning: read_bcal.Rd:27: unknown macro '\abbr'
  Warning: read_chronomodel.Rd:36: unknown macro '\abbr'
  Warning: read_oxcal.Rd:27: unknown macro '\abbr'
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/ArchaeoPhases.Rcheck/00install.out’ for details.
prepare_Rd: read_bcal.Rd:27: unknown macro '\abbr'
prepare_Rd: read_chronomodel.Rd:36: unknown macro '\abbr'
prepare_Rd: read_oxcal.Rd:27: unknown macro '\abbr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'affxparser', 'oligo', 'oligoClasses', 'pdInfoBuilder',
  'AffymetrixDataTestFiles'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R             3.1Mb
    help          1.1Mb
    testScripts   1.1Mb
Packages unavailable to check Rd xrefs: ‘affxparser’, ‘oligo’, ‘oligoClasses’
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Package suggested but not available for checking: ‘GLAD’
Packages suggested but not available for checking:
  'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Package unavailable to check Rd xrefs: ‘GLAD’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 565.0Mb
  sub-directories of 1Mb or more:
    R       5.1Mb
    libs  559.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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    include   6.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   9.0Mb
Package which this enhances but not available for checking: ‘asreml’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘asteRiskData’
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
'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
Specified C++11: please drop specification unless essential
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Running examples in ‘autogam-Ex.R’ failed
The error most likely occurred in:

> ### Name: autogam
> ### Title: Automate the creation of a Generalized Additive Model (GAM)
> ### Aliases: autogam
> 
> ### ** Examples
> 
> autogam(mtcars, 'mpg')
Error in magic(G$y, G$X, msp, G$S, G$off, L = G$L, lsp0 = G$lsp0, G$rank,  : 
  magic, the gcv/ubre optimizer, failed to converge after 400 iterations.
Calls: autogam ... do.call -> <Anonymous> -> estimate.gam -> am.fit -> magic
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
Packages required but not available: 'siggenes', 'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 23.7Mb
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checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 86.2Mb
  sub-directories of 1Mb or more:
    libs  84.1Mb
installed size is 114.9Mb
  sub-directories of 1Mb or more:
    libs  113.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 95.7Mb
  sub-directories of 1Mb or more:
    libs  93.9Mb
GNU make is a SystemRequirements.
installed size is 63.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  61.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   3.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package suggested but not available for checking: ‘fdpbandsdata’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘ArrayExpress’
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
installed size is  5.4Mb
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    data   5.3Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
installed size is  8.0Mb
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Package suggested but not available for checking: ‘reactome.db’
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Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
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checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
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GNU make is a SystemRequirements.
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installed size is  5.4Mb
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installed size is  6.4Mb
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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installed size is 45.9Mb
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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installed size is  8.0Mb
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installed size is 244.5Mb
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
No news entries found.
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'library' or 'require' call not declared from: ‘x’
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Error(s) in re-building vignettes:
--- re-building ‘article.Rnw’ using Sweave
Setting levels: control = No, case = Yes
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-7
Setting levels: control = No, case = Yes
Setting levels: control = No, case = Yes
Loading required package: Biostrings
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

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

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Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

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

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Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

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Error: processing vignette 'article.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'article.Rnw'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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GNU make is a SystemRequirements.
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Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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installed size is  7.0Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘BRugs’
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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
installed size is 96.7Mb
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GNU make is a SystemRequirements.
installed size is  7.8Mb
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'LazyData' is specified without a 'data' directory
installed size is 65.0Mb
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GNU make is a SystemRequirements.
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installed size is 14.5Mb
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'LazyData' is specified without a 'data' directory
installed size is 54.9Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.5Mb
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GNU make is a SystemRequirements.
installed size is 52.3Mb
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GNU make is a SystemRequirements.
installed size is 25.4Mb
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Specified C++11: please drop specification unless essential
installed size is 60.6Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
installed size is 12.9Mb
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checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
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Specified C++11: please drop specification unless essential
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checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘ffbase’
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Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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GNU make is a SystemRequirements.
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installed size is 27.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
installed size is 94.9Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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Package which this enhances but not available for checking: ‘asreml’
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installed size is  5.5Mb
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installed size is  6.1Mb
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installed size is  7.6Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
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installed size is 48.3Mb
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
installed size is  6.5Mb
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Package suggested but not available for checking: ‘IHW’
installed size is 45.1Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
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Found the following significant warnings:

  Warning: 'blandr.output.text' is deprecated.
  Warning: 'blandr.output.text' is deprecated.
  Warning: 'blandr.output.text' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
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Package suggested but not available for checking: ‘cmdstanr’
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GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
installed size is  7.5Mb
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installed size is  7.7Mb
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'LazyData' is specified without a 'data' directory
installed size is 33.9Mb
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GNU make is a SystemRequirements.
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installed size is  7.4Mb
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installed size is 14.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 167.8Mb
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GNU make is a SystemRequirements.
installed size is 97.6Mb
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GNU make is a SystemRequirements.
installed size is 50.4Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
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Package suggested but not available for checking: ‘INLA’
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
installed size is 16.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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Packages suggested but not available for checking:
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Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 10.3Mb
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installed size is 13.1Mb
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installed size is 396.6Mb
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GNU make is a SystemRequirements.
installed size is 93.4Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
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checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
installed size is 52.5Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 45.4Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
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Package suggested but not available for checking: ‘cmdstanr’
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installed size is 11.7Mb
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Specified C++11: please drop specification unless essential
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installed size is 31.9Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is 173.3Mb
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GNU make is a SystemRequirements.
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installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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Package required but not available: ‘GENIE3’

Package suggested but not available for checking: ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
pairwise.matrix: no visible global function definition for ‘%||%’
Undefined global functions or variables:
  %||%
Running examples in ‘bullseye-Ex.R’ failed
The error most likely occurred in:

> ### Name: pair_ace
> ### Title: Alternating conditional expectations correlation
> ### Aliases: pair_ace
> 
> ### ** Examples
> 
>  pair_ace(iris)
Error in rownames(m) %||% paste0("V", seq_along(xindex)) : 
  could not find function "%||%"
Calls: pair_ace -> pairwise -> pairwise.data.frame -> pairwise.matrix
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘calc_pairwise.Rmd’ using rmarkdown

Quitting from lines 44-46 [unnamed-chunk-3] (calc_pairwise.Rmd)
Error: processing vignette 'calc_pairwise.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building ‘calc_pairwise.Rmd’

--- re-building ‘integrating.Rmd’ using rmarkdown

Quitting from lines 57-62 [corrplot_assoc] (integrating.Rmd)
Error: processing vignette 'integrating.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building ‘integrating.Rmd’

--- re-building ‘vis_pairwise.Rmd’ using rmarkdown

Quitting from lines 52-53 [unnamed-chunk-3] (vis_pairwise.Rmd)
Error: processing vignette 'vis_pairwise.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building ‘vis_pairwise.Rmd’

SUMMARY: processing the following files failed:
  ‘calc_pairwise.Rmd’ ‘integrating.Rmd’ ‘vis_pairwise.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘bunching_examples.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_examples.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/bunching.Rcheck/vign_test/bunching/vignettes/bunching_examples.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_examples.log for more info.
--- failed re-building ‘bunching_examples.Rmd’

--- re-building ‘bunching_theory.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_theory.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/bunching.Rcheck/vign_test/bunching/vignettes/bunching_theory.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_theory.log for more info.
--- failed re-building ‘bunching_theory.Rmd’

SUMMARY: processing the following files failed:
  ‘bunching_examples.Rmd’ ‘bunching_theory.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
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installed size is 153.8Mb
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Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘doMPI’
Specified C++11: please drop specification unless essential
installed size is 20.0Mb
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installed size is 44.3Mb
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GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
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Package suggested but not available for checking: ‘ReGenesees’
Package required but not available: ‘aroma.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is 11.0Mb
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
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    captr .1.3
    captr .1.2
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checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
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installed size is 38.3Mb
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 12.2Mb
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
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checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
installed size is  5.1Mb
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GNU make is a SystemRequirements.
installed size is 17.5Mb
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installed size is 22.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.8Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  6.2Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘atp_calculation.Rmd’ using rmarkdown
File mito_glyco_tests.png not found in resource path
Error: processing vignette 'atp_calculation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘atp_calculation.Rmd’

--- re-building ‘ceas.Rmd’ using rmarkdown
--- finished re-building ‘ceas.Rmd’

SUMMARY: processing the following file failed:
  ‘atp_calculation.Rmd’

Error: Vignette re-building failed.
Execution halted
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installed size is 11.3Mb
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Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
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installed size is 37.9Mb
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Malformed Title field: should not end in a period.
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installed size is  6.3Mb
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Specified C++11: please drop specification unless essential
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Package required but not available: ‘pwalign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clhs_0.7-2
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checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
No news entries found.
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Specified C++11: please drop specification unless essential
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Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/cmmr.Rcheck/00install.out’ for details.
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
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Package suggested but not available for checking: ‘tobit1’
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GNU make is a SystemRequirements.
Package required but not available: ‘GenomicInteractions’

Packages suggested but not available for checking:
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Problems with news in ‘NEWS.md’:
No news entries found.
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installed size is  6.9Mb
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Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
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checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
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Packages suggested but not available for checking: 'conosPanel', 'p2data'
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Running examples in ‘conos-Ex.R’ failed
The error most likely occurred in:

> ### Name: Conos
> ### Title: Conos R6 class
> ### Aliases: Conos
> 
> ### ** Examples
> 
> 
> ## ------------------------------------------------
> ## Method `Conos$new`
> ## ------------------------------------------------
> 
> con <- Conos$new(small_panel.preprocessed, n.cores=1)
> 
> 
> ## ------------------------------------------------
> ## Method `Conos$buildGraph`
> ## ------------------------------------------------
> 
> con <- Conos$new(small_panel.preprocessed, n.cores=1)
> con$buildGraph(k=10, k.self=5, space='PCA', ncomps=10, n.odgenes=20, matching.method='mNN',
+     metric='angular', score.component.variance=TRUE, verbose=TRUE)
found 0 out of 1 cached PCA space pairs ... 
running 1 additional PCA space pairs 
Error in irlba::irlba(x, nv = ncomps, nu = 0, center = cm, right_only = FALSE,  : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: <Anonymous> ... FUN -> quickPlainPCA -> lapply -> FUN -> <Anonymous>
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(conos)
  Loading required package: Matrix
  Loading required package: igraph
  
  Attaching package: 'igraph'
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > 
  > testthat::test_check("conos")
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:igraph':
  
      compare
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_functions.R:15:1'): (code run outside of `test_that()`) ────────
  Error in `irlba::irlba(x, nv = ncomps, nu = 0, center = cm, right_only = FALSE, 
      reorth = TRUE)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
       ▆
    1. ├─base::suppressWarnings(con$buildGraph(ncomps = 25)) at test_functions.R:15:1
    2. │ └─base::withCallingHandlers(...)
    3. └─con$buildGraph(ncomps = 25)
    4.   └─private$updatePairs(...)
    5.     └─sccore::plapply(...)
    6.       └─base::lapply(...)
    7.         └─conos (local) FUN(X[[i]], ...)
    8.           └─conos:::quickPlainPCA(...)
    9.             └─base::lapply(...)
   10.               └─conos (local) FUN(X[[i]], ...)
   11.                 └─irlba::irlba(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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    libs   3.1Mb
Packages suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
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'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:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘phyloseq’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProData’
Package suggested but not available for checking: ‘xcms’
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
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fishp: no visible binding for global variable ‘markname’
fishp: no visible binding for global variable ‘sum_chisq’
fishp: no visible binding for global variable ‘sum_z’
pvalues_to_zscores: no visible binding for global variable ‘markname’
tetracorr: no visible binding for global variable ‘PLCORR’
Undefined global functions or variables:
  PLCORR markname sum_chisq sum_z
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
Package required but not available: ‘ctsem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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    libs   5.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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    extdata   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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    doc    2.9Mb
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
  ...
--- re-building ‘cplm.Rnw’ using Sweave
Loading required package: coda
Loading required package: Matrix
Loading required package: splines
Error: processing vignette 'cplm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cplm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.7Mb
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installed size is  8.2Mb
  sub-directories of 1Mb or more:
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installed size is 66.0Mb
  sub-directories of 1Mb or more:
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    libs  64.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.9Mb
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.2Mb
    libs   6.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 41.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
installed size is  6.5Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’
'LazyData' is specified without a 'data' directory
installed size is 29.2Mb
  sub-directories of 1Mb or more:
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installed size is  6.2Mb
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Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
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installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ctsem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ctsem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 202.0Mb
  sub-directories of 1Mb or more:
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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
Package which this enhances but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘TCGAbiolinks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required and available but unsuitable versions:
  'stats', 'tools', 'utils'

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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.2Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Packages which this enhances but not available for checking:
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installed size is 10.5Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 28.2Mb
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installed size is  5.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: jpegReport.Rd:22: unknown macro '\abbr'
  Warning: jpegReport.Rd:50: unknown macro '\abbr'
  Warning: jpegReport.Rd:53: unknown macro '\abbr'
  Warning: jpegReport.Rd:56: unknown macro '\abbr'
  Warning: jpegReport.Rd:58: unknown macro '\abbr'
  Warning: jpegReport.Rd:62: unknown macro '\abbr'
  Warning: pdfReport.Rd:101: unknown macro '\abbr'
  Warning: pngReport.Rd:22: unknown macro '\abbr'
  Warning: pngReport.Rd:50: unknown macro '\abbr'
  Warning: pngReport.Rd:53: unknown macro '\abbr'
  Warning: pngReport.Rd:55: unknown macro '\abbr'
  Warning: pngReport.Rd:59: unknown macro '\abbr'
  Warning: readReportTable.Rd:35: unknown macro '\abbr'
  Warning: readReportTable.Rd:167: unknown macro '\abbr'
  Warning: scanReport.Rd:45: unknown macro '\abbr'
  Warning: scanReport.Rd:60: unknown macro '\abbr'
  Warning: scanReport.Rd:61: unknown macro '\abbr'
  Warning: scanReport.Rd:162: unknown macro '\abbr'
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/D4TAlink.light.Rcheck/00install.out’ for details.
prepare_Rd: jpegReport.Rd:22: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:50: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:53: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:56: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:58: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:62: unknown macro '\abbr'
prepare_Rd: pdfReport.Rd:101: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:22: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:50: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:53: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:55: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:59: unknown macro '\abbr'
prepare_Rd: readReportTable.Rd:35: unknown macro '\abbr'
prepare_Rd: readReportTable.Rd:167: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:45: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:60: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:61: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:162: unknown macro '\abbr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘snpStats’
Package unavailable to check Rd xrefs: ‘snpStats’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
Package suggested but not available for checking: ‘snpStats’
Package unavailable to check Rd xrefs: ‘snpStats’
Package suggested but not available for checking: ‘snpStats’
Package unavailable to check Rd xrefs: ‘snpStats’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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installed size is  7.4Mb
  sub-directories of 1Mb or more:
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    libs   4.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
LazyData DB of 5.1 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   1.8Mb
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.5Mb
Package required but not available: ‘dada2’

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

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
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘BRugs’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 53.3Mb
  sub-directories of 1Mb or more:
    libs  52.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.5Mb
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   2.2Mb
    libs  13.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  35.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package suggested but not available for checking: ‘Rdonlp2’
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.N’ ‘.Nmiss’ ‘.Q1’ ‘.Q3’ ‘.factorN’ ‘.factorNmiss’ ‘.factorQ1’
  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
  ‘.factorsd’ ‘.max’ ‘.mean’ ‘.median’ ‘.min’ ‘.sd’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
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    doc    1.8Mb
    help   1.6Mb
    libs   3.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Package suggested but not available for checking: ‘OSAT’
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'signatureSearch', 'signatureSearchData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'IHW', 'RNASeqPower', 'zFPKM'
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  15.0Mb
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'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  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 48.1Mb
  sub-directories of 1Mb or more:
    libs  47.5Mb
installed size is 69.9Mb
  sub-directories of 1Mb or more:
    libs  69.0Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Package unavailable to check Rd xrefs: ‘airway’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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Package which this enhances but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:158:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘BOLTSSIRR’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
  sub-directories of 1Mb or more:
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installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
installed size is 51.2Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
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Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(EGRETci)
  > test_check("EGRETci")
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (10)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('tests_boot_tests.R:112:3'): paVector ──────────────────────────────
  `paIndexWinter` not equal to 11:13.
  Lengths differ: 4 is not 3
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  Error: Test failures
  Execution halted
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Error(s) in re-building vignettes:
--- re-building ‘ellipticpaper.Rnw’ using Sweave

Attaching package: ‘elliptic’

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

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Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Error: processing vignette 'ellipticpaper.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'ellipticpaper.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm6): Font bbm6 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘ellipticpaper.Rnw’

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

Attaching package: ‘elliptic’

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--- finished re-building ‘residuetheorem.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
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Error(s) in re-building vignettes:
--- re-building ‘jss.Rmd’ using rmarkdown
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
Error: processing vignette 'jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/fairadapt.Rcheck/vign_test/fairadapt/vignettes/jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
--- failed re-building ‘jss.Rmd’

SUMMARY: processing the following file failed:
  ‘jss.Rmd’

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

> ### Name: center.test
> ### Title: Center test
> ### Aliases: center.test
> 
> ### ** Examples
> 
> set.seed(123)
> 
> test <- center.test(MASS::galaxies, mu = 21000, nboot = 100)
> print(test)
-----------------------------------------------
familial test of centers with huber family
-----------------------------------------------
mu = 21000 
posterior probabilities: 
  H0   H1 
0.59 0.41 
optimal decision: indeterminate 
> plot(test)
Error in validObject(.Object) : 
  invalid class “FncBand” object: superclass "mMatrix" not defined in the environment of the object's class
Calls: plot ... initialize -> initialize -> initMatrix -> validObject
Execution halted
Running ‘testthat.R’ [42s/45s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(familial)
  > 
  > test_check("familial")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-center-test.R:27:3'): plot function returns a plot ─────────────
  Error in `validObject(.Object)`: invalid class "FncBand" object: superclass "mMatrix" not defined in the environment of the object's class
  Backtrace:
       ▆
    1. ├─testthat::expect_s3_class(plot(test), "ggplot") at test-center-test.R:27:3
    2. │ └─testthat::quasi_label(enquo(object), arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::plot(test)
    5. └─familial:::plot.center.test(test)
    6.   └─base::lapply(band, bands)
    7.     └─familial (local) FUN(X[[i]], ...)
    8.       ├─base::data.frame(...)
    9.       └─DepthProc::fncGetBand(DepthProc::fncDepth(boot.wide), level)
   10.         └─methods::new("FncBand", bands, index = obj@index, level = band)
   11.           ├─methods::initialize(value, ...)
   12.           └─methods::initialize(value, ...)
   13.             └─methods (local) initMatrix(.Object, ...)
   14.               └─methods::validObject(.Object)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 56-57 [unnamed-chunk-3] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
invalid class "FncBand" object: superclass "mMatrix" not defined in the environment of the object's class
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
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installed size is 11.8Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
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installed size is 18.1Mb
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installed size is 14.9Mb
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installed size is  8.3Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is 47.4Mb
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installed size is  7.2Mb
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Package suggested but not available for checking: ‘coxKM’
installed size is  8.5Mb
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installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
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installed size is 11.2Mb
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Specified C++11: please drop specification unless essential
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installed size is 16.1Mb
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.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
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installed size is 10.4Mb
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GNU make is a SystemRequirements.
installed size is  6.0Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 34.1Mb
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GNU make is a SystemRequirements.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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installed size is 11.0Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is 14.3Mb
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installed size is  6.6Mb
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GNU make is a SystemRequirements.
installed size is 17.0Mb
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installed size is 24.8Mb
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installed size is 12.0Mb
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Package suggested but not available for checking: ‘GEOquery’
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checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
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checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Malformed Description field: should contain one or more complete sentences.
installed size is 34.2Mb
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installed size is  5.5Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbitScraper-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
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checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gridlayout’
installed size is  5.5Mb
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installed size is  9.9Mb
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Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
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installed size is  7.8Mb
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Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
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installed size is 300.5Mb
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GNU make is a SystemRequirements.
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Malformed Description field: should contain one or more complete sentences.
installed size is 27.2Mb
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GNU make is a SystemRequirements.
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installed size is  6.2Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
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Package which this enhances but not available for checking: ‘doMPI’
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GNU make is a SystemRequirements.
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checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
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Running ‘testthat.R’ [72s/75s]
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(GDILM.SEIRS)
  > 
  > test_check("GDILM.SEIRS")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-GDILM_SEIRS_Par_Est.R:4:1'): An example for a real data model fitting ──
  Error in `solve.default(EndY5)`: system is computationally singular: reciprocal condition number = 1.39546e-17
  Backtrace:
      ▆
   1. └─GDILM.SEIRS::GDILM_SEIRS_Par_Est(...) at test-GDILM_SEIRS_Par_Est.R:4:1
   2.   └─GDILM.SEIRS (local) estfun(...)
   3.     ├─base::solve(EndY5)
   4.     └─base::solve.default(EndY5)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
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Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
Running examples in ‘GEC-Ex.R’ failed
The error most likely occurred in:

> ### Name: eep_optim
> ### Title: The Wrapper Function that Returns the Final Estimates from
> ###   Maximum Likelihood Estimation for EEP.
> ### Aliases: eep_optim
> 
> ### ** Examples
> 
> eep_optim(seq(1:100))
Error in stats::optim(init, lower = lower_bound, eep_nll, method = "L-BFGS-B",  : 
  L-BFGS-B needs finite values of 'fn'
Calls: eep_optim -> raw_est_eep -> <Anonymous>
Execution halted
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    libs      1.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘genderdata’
Package required but not available: ‘GEOquery’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rrvgo’
Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘simplifyEnrichment’
Package required but not available: ‘biocViews’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘snpStats’
Specified C++14: please drop specification unless essential
installed size is  6.8Mb
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘reactome.db’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 31.3Mb
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Error(s) in re-building vignettes:
--- re-building ‘geoAr_geofacet.Rmd’ using rmarkdown
File figure/tucmap-1.png not found in resource path
Error: processing vignette 'geoAr_geofacet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘geoAr_geofacet.Rmd’

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

--- re-building ‘georefar.Rmd’ using rmarkdown
--- finished re-building ‘georefar.Rmd’

SUMMARY: processing the following files failed:
  ‘geoAr_geofacet.Rmd’ ‘geoAr_leaflet.Rmd’

Error: Vignette re-building failed.
Execution halted
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installed size is 104.5Mb
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
installed size is  6.8Mb
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    libs   4.8Mb
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘geomarocdata’
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/GeoModels.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘RandomFields’

Package which this enhances but not available for checking: ‘INLA’
Malformed Description field: should contain one or more complete sentences.
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Package suggested but not available for checking: ‘RGtk2’
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Package required but not available: ‘ggmsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
Running examples in ‘ggESDA-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cardiological
> ### Title: Cardiological data example
> ### Aliases: Cardiological
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Cardiological)
> ggInterval_index(Cardiological, aes(x = Syst))
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'tbl_subset_col' not found
Calls: ggInterval_index ... as.data.frame -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggESDA.Rmd’ using rmarkdown
Quitting from lines 47-57 (ggESDA.Rmd) 
Error: processing vignette 'ggESDA.Rmd' failed with diagnostics:
object 'tbl_subset_col' not found
--- failed re-building ‘ggESDA.Rmd’

SUMMARY: processing the following file failed:
  ‘ggESDA.Rmd’

Error: Vignette re-building failed.
Execution halted
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installed size is 11.0Mb
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checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
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checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': ‘scales:::censor’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘productplots:::bound’
  See the note in ?`:::` about the use of this operator.
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Problems with news in ‘NEWS.md’:
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    * Changes all data options to .data to decrease possibility of column naming overlap
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    Win CRAN check results - R Windows
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GNU make is a SystemRequirements.
installed size is  5.8Mb
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No news entries found.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
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GNU make is a SystemRequirements.
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Package required but not available: ‘snpStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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--- re-building ‘custom_ocl_gpuR.Rnw’ using knitr
Error: processing vignette 'custom_ocl_gpuR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'custom_ocl_gpuR.tex' failed.
LaTeX errors:
! Missing $ inserted.
<inserted text> 
                $
l.116 custom_
             ocl_gpuR.R\end{kframe}
! Emergency stop.
<inserted text> 
                $
l.116 custom_
             ocl_gpuR.R\end{kframe}
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘custom_ocl_gpuR.Rnw’

--- re-building ‘gpuR.Rnw’ using knitr
--- finished re-building ‘gpuR.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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Package suggested but not available for checking: ‘monocle’
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GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for ‘gg’ with
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Package required but not available: ‘EnsDb.Hsapiens.v75’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.ga.breed’ ‘.ga.fitness’ ‘.ga.init’ ‘.ga.mutate’ ‘.ga.step’
  ‘.ga.weight’
Package required but not available: ‘handwriterRF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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GNU make is a SystemRequirements.
Running examples in ‘HCD-Ex.R’ failed
The error most likely occurred in:

> ### Name: HCD
> ### Title: hierarchical community detection with recursive spectral methods
> ### Aliases: HCD
> ### Keywords: HCD BTSBM
> 
> ### ** Examples
> 
> dt <- BTSBM(n=1600,d=4,a.seq=0.2^seq(0,4),lambda=50)
> A <- dt$A.list[[1]]
> # you can try various versions of the algorithm as below: the Fix is fastest and ECV is slowest.
> system.time(HCD.result <- HCD(A,method="SC",stopping="Fix",D=4))
Begin clustering....
Error in irlba(f, nu = 2, nv = 2) : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: system.time -> HCD -> break.cl.sp -> irlba
Timing stopped at: 0.006 0 0.006
Execution halted
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Running examples in ‘healthyR.ai-Ex.R’ failed
The error most likely occurred in:

> ### Name: hai_umap_list
> ### Title: UMAP Projection
> ### Aliases: hai_umap_list umap_list
> 
> ### ** Examples
> 
> library(healthyR.data)

== Welcome to healthyR.data ===========================================================================
If you find this package useful, please leave a star: 
   https://github.com/spsanderson/healthyR.data'

If you encounter a bug or want to request an enhancement please file an issue at:
   https://github.com/spsanderson/healthyR.data/issues

Thank you for using healthyR.data
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(broom)
> 
> data_tbl <- healthyR_data %>%
+   filter(ip_op_flag == "I") %>%
+   filter(payer_grouping != "Medicare B") %>%
+   filter(payer_grouping != "?") %>%
+   select(service_line, payer_grouping) %>%
+   mutate(record = 1) %>%
+   as_tibble()
> 
> uit_tbl <- hai_kmeans_user_item_tbl(
+   .data = data_tbl,
+   .row_input = service_line,
+   .col_input = payer_grouping,
+   .record_input = record
+ )
> 
> kmm_tbl <- hai_kmeans_mapped_tbl(uit_tbl)
> 
> umap_list(.data = uit_tbl, kmm_tbl, 3)
Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: umap_list ... irlba_tsvd_normalized_laplacian_init -> irlba_spectral_tsvd
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘auto-kmeans.Rmd’ using rmarkdown
--- finished re-building ‘auto-kmeans.Rmd’

--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’

--- re-building ‘kmeans-umap.Rmd’ using rmarkdown

Quitting from lines 147-148 [umap_list] (kmeans-umap.Rmd)
Error: processing vignette 'kmeans-umap.Rmd' failed with diagnostics:
function 'as_cholmod_sparse' not provided by package 'Matrix'
--- failed re-building ‘kmeans-umap.Rmd’

SUMMARY: processing the following file failed:
  ‘kmeans-umap.Rmd’

Error: Vignette re-building failed.
Execution halted
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Package required and available but unsuitable version: ‘healthyR.ai’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Heatplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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GNU make is a SystemRequirements.
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html_describe_con: multiple local function definitions for ‘g’ with
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/hoardeR.Rcheck/00install.out’ for details.
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Running examples in ‘iGraphMatch-Ex.R’ failed
The error most likely occurred in:

> ### Name: center_graph
> ### Title: Center adjacency matrix
> ### Aliases: center_graph
> 
> ### ** Examples
> 
> A <- sample_correlated_gnp_pair(n = 10, corr = .5, p = .5)$graph1
> center_graph(A, scheme = "naive")
10 x 10 sparse Matrix of class "dgCMatrix"
                         
 [1,] . 1 . . . 1 . 1 1 .
 [2,] 1 . 1 . 1 1 1 . 1 .
 [3,] . 1 . . 1 1 . . 1 .
 [4,] . . . . . . . . . 1
 [5,] . 1 1 . . . 1 1 1 .
 [6,] 1 1 1 . . . 1 1 1 1
 [7,] . 1 . . 1 1 . . 1 1
 [8,] 1 . . . 1 1 . . . 1
 [9,] 1 1 1 . 1 1 1 . . .
[10,] . . . 1 . 1 1 1 . .
> center_graph(A, scheme = "center")
Sparse part
10 x 10 sparse Matrix of class "dgCMatrix"
                         
 [1,] . 2 . . . 2 . 2 2 .
 [2,] 2 . 2 . 2 2 2 . 2 .
 [3,] . 2 . . 2 2 . . 2 .
 [4,] . . . . . . . . . 2
 [5,] . 2 2 . . . 2 2 2 .
 [6,] 2 2 2 . . . 2 2 2 2
 [7,] . 2 . . 2 2 . . 2 2
 [8,] 2 . . . 2 2 . . . 2
 [9,] 2 2 2 . 2 2 2 . . .
[10,] . . . 2 . 2 2 2 . .
plus left factor
10 x 1 Matrix of class "dgeMatrix"
      [,1]
 [1,]   -1
 [2,]   -1
 [3,]   -1
 [4,]   -1
 [5,]   -1
 [6,]   -1
 [7,]   -1
 [8,]   -1
 [9,]   -1
[10,]   -1
times right factor transpose
10 x 1 Matrix of class "dgeMatrix"
      [,1]
 [1,]    1
 [2,]    1
 [3,]    1
 [4,]    1
 [5,]    1
 [6,]    1
 [7,]    1
 [8,]    1
 [9,]    1
[10,]    1
> center_graph(A, scheme = 2)
Error in irlba::irlba(a, rank) : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: center_graph -> splr -> splr -> <Anonymous>
Execution halted
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Malformed Description field: should contain one or more complete sentences.
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Packages required but not available: 'siggenes', 'RankProd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
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No news entries found.
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Malformed Title field: should not end in a period.
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Specified C++11: please drop specification unless essential
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Errors in running code in vignettes:
when running code in ‘PennsylvaniaWarbler.Rmd’
  ...
Loading required package: PointedSDMs
Loading required package: inlabru
Loading required package: fmesher
Loading required package: R6

> library(USAboundaries)

  When sourcing ‘PennsylvaniaWarbler.R’:
Error: there is no package called ‘USAboundaries’
Execution halted
when running code in ‘RedList.Rmd’
  ...
Loading required package: PointedSDMs
Loading required package: inlabru
Loading required package: fmesher
Loading required package: R6

> library(INLA)

  When sourcing ‘RedList.R’:
Error: there is no package called ‘INLA’
Execution halted
when running code in ‘Richness.Rmd’
  ...
Loading required package: PointedSDMs
Loading required package: inlabru
Loading required package: fmesher
Loading required package: R6

> library(INLA)

  When sourcing ‘Richness.R’:
Error: there is no package called ‘INLA’
Execution halted

  ‘PennsylvaniaWarbler.Rmd’ using ‘UTF-8’... failed
  ‘RedList.Rmd’ using ‘UTF-8’... failed
  ‘Richness.Rmd’ using ‘UTF-8’... failed
Specified C++11: please drop specification unless essential
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘surveyspec’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data           1.4Mb
    libs           1.8Mb
    shiny-server   1.0Mb
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rhdf5’
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Package suggested but not available for checking: ‘Rmpi’
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running ‘edge.R’ [1s/1s]
  Running ‘prcomp.r’ [1s/1s]
  Running ‘ssvd.R’ [1s/1s]
  Running ‘svdr.R’ [1s/1s]
  Running ‘test.R’ [1s/1s]
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
  + 
  +   # test for https://github.com/bwlewis/irlba/issues/42
  +   set.seed(1234)
  +   a <- matrix(rnorm(10000), ncol=20)
  +   center <- runif(ncol(a))
  +   scale <- runif(ncol(a))
  +   L <- irlba(a, 5, scale=scale, center=center, fastpath=FAST)
  +   S <- svd(scale(a, center=center, scale=scale))
  +   if (isTRUE(max(abs(S$d[1:5] - L$d)) > 1e-3))
  +   {
  +     stop("Failed scale + center test fastpath=", FAST)
  +   }
  + }
  Error: Failed tprolate test fastpath=FALSE
  Execution halted
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xcms’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   3.3Mb
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
installed size is 93.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
    libs  88.2Mb
GNU make is a SystemRequirements.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  13.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘iucnrdata’
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          17.0Mb
GNU make is a SystemRequirements.
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  35.2Mb
Packages suggested but not available for checking: 'lfa', 'gcatest'
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   4.0Mb
    help      2.0Mb
installed size is 102.7Mb
  sub-directories of 1Mb or more:
    libs  101.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.8Mb
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Specified C++11: please drop specification unless essential
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    i18n   6.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.1Mb
Package suggested but not available for checking: ‘remMap’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘PSCBS’
Package unavailable to check Rd xrefs: ‘PSCBS’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  32.8Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    examples      2.8Mb
    htmlwidgets   1.1Mb
    www           2.7Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kanjistat.data’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   8.0Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’ using Sweave
Error: processing vignette 'Instruction_of_functions_of_R_package_KINSIMU.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Instruction_of_functions_of_R_package_KINSIMU.tex' failed.
LaTeX errors:
! LaTeX Error: Command \gather already defined.
               Or name \end... illegal, see p.192 of the manual.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! Emergency stop.
 ...                                              
                                                  
l.1560 }
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RGeostats’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pwalign’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kadmin’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.8Mb
'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:
    R      2.0Mb
    doc    1.7Mb
    help   1.1Mb
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_latent2likert.Rmd’ using rmarkdown
File man/figures/courses-grouped-min.png not found in resource path
Error: processing vignette 'using_latent2likert.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘using_latent2likert.Rmd’

SUMMARY: processing the following file failed:
  ‘using_latent2likert.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘mixAK’
Package unavailable to check Rd xrefs: ‘mixAK’
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'xcms', 'MSnbase'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘VariantAnnotation’
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 72.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  67.6Mb
GNU make is a SystemRequirements.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 46.2Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  43.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  10.5Mb
installed size is 93.8Mb
  sub-directories of 1Mb or more:
    libs  92.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
installed size is 43.5Mb
  sub-directories of 1Mb or more:
    libs  43.3Mb
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      8.7Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
installed size is 68.4Mb
  sub-directories of 1Mb or more:
    libs  67.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘org.Mm.eg.db’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 22-30 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs      22.1Mb
    testdata   1.3Mb
installed size is 57.8Mb
  sub-directories of 1Mb or more:
    libs  56.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R              2.1Mb
    doc-overview   2.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   5.2Mb
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Specified C++11: please drop specification unless essential
installed size is 65.4Mb
  sub-directories of 1Mb or more:
    libs  65.0Mb
'LazyData' is specified without a 'data' directory
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  32.7Mb
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

SUMMARY: processing the following file failed:
  ‘localsolver.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
installed size is 27.3Mb
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Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’
Specified C++11: please drop specification unless essential
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 19.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
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    libs   5.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘QSutils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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    data   5.0Mb
Specified C++11: please drop specification unless essential
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installed size is  5.6Mb
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installed size is  5.2Mb
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    libs   3.6Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 92.5Mb
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Package suggested but not available for checking: ‘kerdiest’
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installed size is 10.6Mb
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installed size is 50.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error: package or namespace load failed for ‘LSTbook’:
 .onLoad failed in loadNamespace() for 'LSTbook', details:
  call: loadNamespace(name)
  error: there is no package called ‘ggformula’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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installed size is  6.2Mb
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installed size is  6.2Mb
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installed size is  6.0Mb
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Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘depth’
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installed size is 24.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 32.2Mb
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘quitte’
installed size is  6.8Mb
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installed size is 55.9Mb
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'LazyData' is specified without a 'data' directory
installed size is 24.2Mb
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Package suggested but not available for checking: ‘dittoSeq’
Packages suggested but not available for checking:
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocCheck’
installed size is  9.7Mb
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    R      2.0Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 10.5Mb
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    libs   9.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      3.3Mb
    extdata   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
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    doc   6.9Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
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    data   1.2Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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    libs   5.9Mb
installed size is 33.5Mb
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Specified C++14: please drop specification unless essential
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
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    htmlwidgets   3.5Mb
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R   8.4Mb
Specified C++11: please drop specification unless essential
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   4.7Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
GNU make is a SystemRequirements.
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
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installed size is 15.3Mb
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    libs      11.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    libs   3.4Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘marssTMB’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.NCBI.GRCh38', 'clusterProfiler', 'org.Mm.eg.db',
  'wiggleplotr'
installed size is  8.6Mb
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installed size is  8.3Mb
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    libs   7.4Mb
installed size is 49.1Mb
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'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 13.2Mb
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Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
installed size is  8.7Mb
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Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
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installed size is 11.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.7Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
qr.X: no visible binding for global variable ‘R’
Undefined global functions or variables:
  R
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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    data   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.8Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
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checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
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installed size is 34.3Mb
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    libs  33.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 17.2Mb
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    libs  16.7Mb
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  15.9Mb
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘cmdstanr’
installed size is  6.8Mb
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'LazyData' is specified without a 'data' directory
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
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checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
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checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
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installed size is 11.3Mb
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Package suggested but not available for checking: ‘RGtk2’
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'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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    doc       1.9Mb
    extdata   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Package suggested but not available for checking: ‘cmdstanr’
installed size is 64.1Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 50.4Mb
  sub-directories of 1Mb or more:
    libs  49.1Mb
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
ADPopSel: no visible global function definition for ‘%dorng%’
ADRand: no visible global function definition for ‘%dorng%’
ADSSMod: no visible global function definition for ‘%dorng%’
ADTreatSel: no visible global function definition for ‘%dorng%’
ClustRand: no visible global function definition for ‘%dorng%’
EventPred: no visible global function definition for ‘%dorng%’
FutRuleNCores: no visible global function definition for ‘%dorng%’
MultAdj1NCores: no visible global function definition for ‘%dorng%’
MultAdj2NCores: no visible global function definition for ‘%dorng%’
MultAdj3NCores: no visible global function definition for ‘%dorng%’
Undefined global functions or variables:
  %dorng%
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 155.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 22.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
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Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 107.1Mb
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GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'ropls', 'xcms'
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
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    help   2.2Mb
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
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    examples  10.3Mb
Packages suggested but not available for checking:
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installed size is  5.2Mb
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installed size is 21.4Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘InteractiveComplexHeatmap’
installed size is 60.3Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 12.8Mb
  sub-directories of 1Mb or more:
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installed size is 27.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 19.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'
installed size is  7.3Mb
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Specified C++11: please drop specification unless essential
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dada2’
Package required but not available: ‘microbiome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19',
  'BSgenome.Mmusculus.UCSC.mm10'
Running examples in ‘MicroSEC-Ex.R’ failed
The error most likely occurred in:

> ### Name: fun_load_genome
> ### Title: Genome loading function.
> ### Aliases: fun_load_genome
> 
> ### ** Examples
> 
> fun_load_genome("Human")
Error: Install BSgenome.Hsapiens.UCSC.hg38 package.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using rmarkdown

Quitting from lines 125-195 [analysis] (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'BSgenome.Hsapiens.UCSC.hg38'
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Execution halted
installed size is 20.5Mb
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    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘midfielddata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘gurobi’
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
Package required but not available: ‘InteractiveComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  22.4Mb
installed size is 42.7Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 41.2Mb
  sub-directories of 1Mb or more:
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    redengine  39.6Mb
'LazyData' is specified without a 'data' directory
installed size is 119.3Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Package unavailable to check Rd xrefs: ‘mixAK’
Package required but not available: ‘dada2’

Packages suggested but not available for checking: 'ANCOMBC', 'mia'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   1.2Mb
    libs      1.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Packages suggested but not available for checking:
  'karyoploteR', 'regioneR'
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Package which this enhances but not available for checking: ‘pbdMPI’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
installed size is 41.3Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) mixmeta.ml.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mixRasch’
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'minfi', 'GEOquery', 'IlluminaHumanMethylation450kmanifest'
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 243.0Mb
  sub-directories of 1Mb or more:
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    libs     232.6Mb
Package suggested but not available for checking: ‘mlr3proba’
Package unavailable to check Rd xrefs: ‘mlr3proba’
Package suggested but not available for checking: ‘Rmpi’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 134.9Mb
  sub-directories of 1Mb or more:
    doc     1.2Mb
    libs  132.9Mb
GNU make is a SystemRequirements.
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    libs  49.7Mb
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  27.9Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
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    shiny   14.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  15.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
'LazyData' is specified without a 'data' directory
installed size is 121.1Mb
  sub-directories of 1Mb or more:
    libs  119.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
'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:
    libs  10.4Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'doMPI', 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Package required but not available: ‘doMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR'
'LazyData' is specified without a 'data' directory
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
installed size is  9.8Mb
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    libs   8.2Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    libs   4.6Mb
installed size is  7.2Mb
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    libs   6.6Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
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Package suggested but not available for checking: ‘lixoftConnectors’
installed size is  5.9Mb
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    theo   1.1Mb
GNU make is a SystemRequirements.
installed size is 10.8Mb
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    data   2.0Mb
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
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    libs     3.0Mb
    raster   2.2Mb
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
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    data   2.3Mb
    libs   2.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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Error: package or namespace load failed for ‘movieROC’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘knitr’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, cha
Execution halted
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error: there is no package called ‘knitr’
Call sequence:
14: doWithOneRestart(return(expr), restart)
13: withOneRestart(expr, restarts[[1L]])
12: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
11: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
10: asNamespace(ns)
9: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
7: asNamespace(ns)
6: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPat
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  5.6Mb
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    libs   5.0Mb
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
Package suggested but not available for checking: ‘rhdf5’
installed size is 10.6Mb
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    libs   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 92.3Mb
  sub-directories of 1Mb or more:
    libs  91.9Mb
GNU make is a SystemRequirements.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  12.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   4.5Mb
    libs   3.9Mb
installed size is 49.3Mb
  sub-directories of 1Mb or more:
    libs  48.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
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    libs  17.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   7.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'switchBox', 'leukemiasEset'
Package suggested but not available for checking: ‘cmdstanr’
installed size is  7.9Mb
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    doc   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is 12.5Mb
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    libs  11.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is 98.0Mb
  sub-directories of 1Mb or more:
    libs  97.7Mb
installed size is 271.4Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.2Mb
    libs  264.5Mb
GNU make is a SystemRequirements.
installed size is  6.1Mb
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    libs   4.7Mb
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building ‘multipol.Rnw’ using Sweave
Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

The following object is masked from ‘package:stats’:

    deriv

The following object is masked from ‘package:base’:

    single

Loading required package: polynom
Error: processing vignette 'multipol.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'multipol.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘multipol.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
--- re-building ‘cias.Rnw’ using Sweave

Attaching package: ‘multivator’

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

    levels, rbind

--- finished re-building ‘cias.Rnw’

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

Attaching package: 'multivator'

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

    levels, rbind

Error: processing vignette 'multivator.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'multivator.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'multivator.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package suggested but not available for checking: ‘cmdstanr’
installed size is  6.6Mb
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    R      1.9Mb
    doc    2.0Mb
    libs   1.8Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
Packages suggested but not available for checking: 'BioNet', 'DLBCL'
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   6.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    libs   5.7Mb
installed size is  9.3Mb
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    libs   9.2Mb
Package which this enhances but not available for checking: ‘asreml’
installed size is 16.3Mb
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    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    23.3Mb
    models   1.1Mb
installed size is  6.6Mb
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    libs   4.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Specified C++11: please drop specification unless essential
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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    data   4.6Mb
    doc    1.7Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.5Mb
    libs   5.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rhdf5’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Specified C++11: please drop specification unless essential
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Specified C++11: please drop specification unless essential
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.5Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  17.3Mb
Package suggested but not available for checking: ‘fastshp’
installed size is  6.7Mb
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    doc    1.6Mb
    libs   4.9Mb
installed size is  8.3Mb
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    libs   5.5Mb
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 243.5Mb
  sub-directories of 1Mb or more:
    libs  242.8Mb
GNU make is a SystemRequirements.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Specified C++14: please drop specification unless essential
'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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    4.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is 43.3Mb
  sub-directories of 1Mb or more:
    CppCode        3.5Mb
    R              8.1Mb
    classic-bugs   1.5Mb
    include       11.5Mb
    libs          17.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Specified C++11: please drop specification unless essential
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.7Mb
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  5.7Mb
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    doc   5.5Mb
Package suggested but not available for checking: ‘doMPI’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘simpar’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
    mods   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    libs       3.2Mb
    tinytest   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [12s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    6. └─npi::npi_search(city = "Atlanta", limit = 1)
    7.   └─npi:::npi_process_results(...)
    8.     └─npi:::npi_control_requests(params, user_n)
    9.       └─npi:::npi_get_results(results = results, query = query)
   10.         └─npi:::npi_get(npi_url(), query = ...)
   11.           └─npi:::npi_api("GET", url, ...)
   12.             └─httr (local) FUN(url, ..., config = c(npi_config(), config))
   13.               └─httr:::request_perform(req, hu$handle$handle)
   14.                 ├─httr:::request_fetch(req$output, req$url, handle)
   15.                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   16.                   └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced-use.Rmd’ using rmarkdown
Quitting from lines 39-46 (advanced-use.Rmd) 
Error: processing vignette 'advanced-use.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `curl::curl_fetch_memory()`:
! Could not resolve host: npiregistry.cms.hhs.gov
--- failed re-building ‘advanced-use.Rmd’

--- re-building ‘npi.Rmd’ using rmarkdown
Quitting from lines 34-36 (npi.Rmd) 
Error: processing vignette 'npi.Rmd' failed with diagnostics:
Could not resolve host: npiregistry.cms.hhs.gov
--- failed re-building ‘npi.Rmd’

SUMMARY: processing the following files failed:
  ‘advanced-use.Rmd’ ‘npi.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs  15.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    doc       5.7Mb
    extdata   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.6Mb
    test_files   4.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.4Mb
    libs   5.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.9Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 99.0Mb
  sub-directories of 1Mb or more:
    libs  98.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
'LazyData' is specified without a 'data' directory
Fatal error: cannot create 'R_TempDir'
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Warning in file(open = "w+") :
  cannot open file '/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpYdXjvw/Rfee3b1220180e': No space left on device
Error in file(open = "w+") : cannot open the connection
Calls: <Anonymous> -> .load_namespace_quietly -> .try_quietly -> file
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  44.0Mb
GNU make is a SystemRequirements.
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  40.1Mb
GNU make is a SystemRequirements.
Package required but not available: ‘TCGAbiolinks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    exampledata   1.5Mb
    libs          3.6Mb
GNU make is a SystemRequirements.
installed size is 31.3Mb
  sub-directories of 1Mb or more:
    libs   21.0Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 273.4Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    data      1.4Mb
    libs    261.6Mb
    models    4.7Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Package suggested but not available for checking: ‘openNLPmodels.en’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.4Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   9.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   1.2Mb
    libs      5.1Mb
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs     33.6Mb
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'gurobi', 'lpsymphony'
Specified C++11: please drop specification unless essential
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.1Mb
Package suggested but not available for checking: ‘rrelaxiv’
Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   6.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcplex’
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Package suggested but not available for checking: ‘scde’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    library   8.5Mb
Package suggested but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/PAMhm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MicrobiotaProcess’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘Rmpi’
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs  43.0Mb
installed size is 84.1Mb
  sub-directories of 1Mb or more:
    libs  83.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.5Mb
Package required but not available: ‘ggkegg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘anomalize’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      7.9Mb
    help   3.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    help   4.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      3.3Mb
    help   3.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   4.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   4.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/pbdMPI.Rcheck/00install.out’ for details.
Package required but not available: ‘pbdMPI’

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  6.8Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.2Mb
    libs   1.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      3.0Mb
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 133.1Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
    libs  129.4Mb
GNU make is a SystemRequirements.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.0Mb
Specified C++11: please drop specification unless essential
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/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
Package suggested but not available for checking: ‘ggtreeExtra’
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘PythonInR’
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs    8.4Mb
    share  12.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Package suggested but not available for checking: ‘georob’
Package suggested but not available for checking: ‘snpStats’
installed size is 136.3Mb
  sub-directories of 1Mb or more:
    libs  135.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   7.0Mb
installed size is 52.4Mb
  sub-directories of 1Mb or more:
    libs  51.2Mb
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
GNU make is a SystemRequirements.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Package required but not available: ‘snpStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
installed size is 48.2Mb
  sub-directories of 1Mb or more:
    libs  47.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
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    libs   3.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
installed size is 84.8Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘phyloseq’
installed size is 62.9Mb
  sub-directories of 1Mb or more:
    libs  62.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    2.1Mb
Package suggested but not available for checking: ‘INLA’
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
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Running ‘testthat.R’ [14s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pipeflow)
  > lgr::suspend_logging()
  > 
  > options(Ncpus = 6)
  > 
  > test_check("pipeflow")
  Starting 6 test processes
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 906 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_pipeflow_log.R:11:5'): time can be formatted to contain GMT offset ──
  `hasCorrectFormat` is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 906 ]
  Error: Test failures
  Execution halted
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installed size is  5.2Mb
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installed size is  9.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
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Package required but not available: ‘VariantAnnotation’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘slingshot’
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Specified C++11: please drop specification unless essential
installed size is  7.2Mb
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installed size is  5.7Mb
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installed size is 17.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  7.0Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
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Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
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Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Errors in running code in vignettes:
when running code in ‘Marked_Point_Process.Rmd’
  ...

> library(ggplot2)

> library(inlabru)

> library(INLA)

  When sourcing ‘Marked_Point_Process.R’:
Error: there is no package called ‘INLA’
Execution halted
when running code in ‘Setophaga.Rmd’
  ...

> args(datasetOut)
function (model, dataset, predictions = TRUE) 
NULL

> library(INLA)

  When sourcing ‘Setophaga.R’:
Error: there is no package called ‘INLA’
Execution halted
when running code in ‘Solitary_tinamou.Rmd’
  ...
terra 1.7.78

> library(ggpolypath)
Loading required package: ggplot2

> library(INLA)

  When sourcing ‘Solitary_tinamou.R’:
Error: there is no package called ‘INLA’
Execution halted
when running code in ‘Spatiotemporal_example.Rmd’
  ...

> library(ggplot2)

> library(spocc)

> library(INLA)

  When sourcing ‘Spatiotemporal_example.R’:
Error: there is no package called ‘INLA’
Execution halted

  ‘Marked_Point_Process.Rmd’ using ‘UTF-8’... failed
  ‘Setophaga.Rmd’ using ‘UTF-8’... failed
  ‘Solitary_tinamou.Rmd’ using ‘UTF-8’... failed
  ‘Spatiotemporal_example.Rmd’ using ‘UTF-8’... failed
'LazyData' is specified without a 'data' directory
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘pollimetrydata’
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installed size is  6.3Mb
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Package suggested but not available for checking: ‘VariantAnnotation’
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Package unavailable to check Rd xrefs: ‘VariantAnnotation’
installed size is  5.2Mb
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installed size is 19.5Mb
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installed size is  7.0Mb
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installed size is 63.1Mb
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
No news entries found.
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
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Specified C++11: please drop specification unless essential
installed size is 12.1Mb
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Specified C++11: please drop specification unless essential
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Specified C++11: please drop specification unless essential
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Problems with news in ‘NEWS.md’:
No news entries found.
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Specified C++11: please drop specification unless essential
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installed size is 10.5Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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installed size is 28.4Mb
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iclust: no visible binding for global variable ‘use’
Undefined global functions or variables:
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GNU make is a SystemRequirements.
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checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
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Problems with news in ‘NEWS.md’:
No news entries found.
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GNU make is a SystemRequirements.
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Malformed Description field: should contain one or more complete sentences.
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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Packages suggested but not available for checking: 'batchelor', 'slingshot'
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'LazyData' is specified without a 'data' directory
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installed size is  5.7Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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installed size is 45.8Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown
Quitting from lines 425-461 (ragtop_convertibles_in_r.Rmd) 
Error: processing vignette 'ragtop_convertibles_in_r.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘ragtop_convertibles_in_r.Rmd’

SUMMARY: processing the following file failed:
  ‘ragtop_convertibles_in_r.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 34.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
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    super-tiny-icons   1.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   7.1Mb
Packages suggested but not available for checking: 'xcms', 'MSnbase'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Spectra’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
'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
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      9.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   7.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 66.2Mb
  sub-directories of 1Mb or more:
    libs  65.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    rstudio   1.6Mb
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    etc    1.9Mb
    po     1.2Mb
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs  11.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
'LazyData' is specified without a 'data' directory
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  24.7Mb
Package suggested but not available for checking: ‘raybevel’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   3.3Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      3.8Mb
GNU make is a SystemRequirements.
installed size is 66.0Mb
  sub-directories of 1Mb or more:
    libs  64.0Mb
GNU make is a SystemRequirements.
installed size is 58.2Mb
  sub-directories of 1Mb or more:
    libs  57.6Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rhdf5’
'LazyData' is specified without a 'data' directory
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    blp   20.1Mb
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 67.9Mb
  sub-directories of 1Mb or more:
    libs  67.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    cont  20.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.5Mb
    po    2.4Mb
Package suggested but not available for checking: ‘conics’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Packages suggested but not available for checking:
  'ROntoTools', 'hgu133plus2.db', 'pd.hg.u133.plus.2', 'oligo'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/Rcplex.Rcheck/00install.out’ for details.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  17.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
    libs      2.2Mb
Specified C++11: please drop specification unless essential
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 39.7Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
    libs      1.8Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    include  45.6Mb
Specified C++11: please drop specification unless essential
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    include   9.5Mb
    libs     24.1Mb
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/RcppMeCab.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Specified C++11: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      5.2Mb
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    include        7.2Mb
    jsonexamples   3.8Mb
    libs          11.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      5.6Mb
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      4.6Mb
    data   1.5Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Running examples in ‘realTimeloads-Ex.R’ failed
The error most likely occurred in:

> ### Name: impute_data
> ### Title: Returns x with gaps imputed using ARIMA and Decision Trees,
> ###   optional uncertainty estimation using Monte Carlo resampling
> ### Aliases: impute_data
> 
> ### ** Examples
> 
> # Impute non-tidal data
> time <- realTimeloads::ExampleData$Sediment_Samples$time
> xo <- realTimeloads::ExampleData$Sediment_Samples$SSCxs_mg_per_liter
> Q <- realTimeloads::ExampleData$Discharge$Discharge_m_cubed_per_s
> idata <- sample(1:length(xo),round(length(xo)*0.5),replace=FALSE)
> x <- rep(NA,length(xo))
> x[idata] <- xo[idata] # simulated samples
> flow_concentrtion_ratio <- imputeTS::na_interpolation(Q/x)
> Xreg <- cbind(Q,flow_concentrtion_ratio)
> Output <- impute_data(time,x,Xreg,MC = 10,ptrain = 0.8)
Error in optim(init[mask], getLike, method = "L-BFGS-B", lower = rep(0,  : 
  L-BFGS-B needs finite values of 'fn'
Calls: impute_data -> <Anonymous> -> <Anonymous> -> optim
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'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.
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   3.1Mb
installed size is 41.1Mb
  sub-directories of 1Mb or more:
    libs        1.4Mb
    redengine  39.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Package suggested but not available for checking: ‘Rmpi’
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  14.5Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      4.6Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpi’

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
Package which this enhances but not available for checking: ‘Rcplex’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'PADOG', 'GSVA'
Packages unavailable to check Rd xrefs: ‘GSVA’, ‘PADOG’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.8Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.2Mb
    libs  13.9Mb
GNU make is a SystemRequirements.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
Package suggested but not available for checking: ‘resourcecodedata’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    libs  42.0Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs     24.1Mb
    models    1.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Package suggested but not available for checking: ‘ccdata’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RevGadgets’
'LazyData' is specified without 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 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  43.2Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'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
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    fonts   1.5Mb
    libs   23.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  16.2Mb
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.4Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   8.7Mb
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 55.9Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs     51.6Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
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installed size is 28.3Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  23.8Mb
'LazyData' is specified without a 'data' directory
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  44.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   17.1Mb
'LazyData' is specified without a 'data' directory
installed size is 160.6Mb
  sub-directories of 1Mb or more:
    libs  159.6Mb
GNU make is a SystemRequirements.
installed size is 70.9Mb
  sub-directories of 1Mb or more:
    include   7.1Mb
    lib      37.1Mb
    libs     26.3Mb
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'DoubletFinder', 'EnhancedVolcano', 'RcppPlanc', 'reactome.db'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rnaturalearthhires’
'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:
    libs   9.0Mb
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/RMark.Rcheck/00install.out’ for details.
Warning: Software mark not found in path.
         If you have mark executable, you will need to set MarkPath object to its location (e.g. MarkPath="C:/Users/Jeff Laake/Desktop"

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
installed size is 132.0Mb
  sub-directories of 1Mb or more:
    libs  131.6Mb
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/RmecabKo.Rcheck/00install.out’ for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   6.0Mb
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
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    libs       1.2Mb
    minizinc   3.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 38.9Mb
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    libs  38.0Mb
installed size is 27.5Mb
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    libs  27.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 84.3Mb
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Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
GNU make is a SystemRequirements.
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  29.9Mb
Package required but not available: ‘R4RNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Package suggested but not available for checking: ‘recount3’
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
Packages which this enhances but not available for checking:
  'pbdMPI', 'Rmpi'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Packages unavailable to check Rd xrefs: ‘pbdMPI’, ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 119.5Mb
  sub-directories of 1Mb or more:
    extdata    2.0Mb
    libs     117.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   1.7Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R  11.3Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
installed size is  6.9Mb
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    libs   6.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 96.1Mb
  sub-directories of 1Mb or more:
    libs  95.3Mb
GNU make is a SystemRequirements.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
Specified C++11: please drop specification unless essential
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
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    libs              5.1Mb
    simulationStudy   1.5Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    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
sh: cmake: command not found
------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

 - installr::install.cmake()  (Windows; inside the R console)
 - yum install cmake          (Fedora/CentOS; inside a terminal)
 - apt install cmake          (Debian/Ubuntu; inside a terminal)
 - brew install cmake         (MacOS; inside a terminal with Homebrew)
 - port install cmake         (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: <https://cmake.org/>

-------------------------------------------------------


It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/ROracle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    libs   9.6Mb
Package suggested but not available for checking: ‘RandomFields’
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
installed size is 49.3Mb
  sub-directories of 1Mb or more:
    libs  49.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 103.5Mb
  sub-directories of 1Mb or more:
    libs  102.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
Errors in running code in vignettes:
when running code in ‘Using.RRPP.Rmd’
  ...
> fit.par <- lm(fit$call$f1, data = fit$LM$data)

> all.equal(fit$LM$coefficients, fit.par$coefficients)
[1] TRUE

> summary(manova(fit.par))

  When sourcing ‘Using.RRPP.R’:
Error: residuals have rank 49 < 112
Execution halted

  ‘ANOVA.vs.MANOVA.Rmd’ using ‘UTF-8’... [18s/28s] OK
  ‘Using.RRPP.Rmd’ using ‘UTF-8’... failed
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  24.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    help   1.5Mb
Specified C++11: please drop specification unless essential
installed size is 46.6Mb
  sub-directories of 1Mb or more:
    libs  46.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 296.7Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.7Mb
    libs  289.2Mb
GNU make is a SystemRequirements.
installed size is 94.9Mb
  sub-directories of 1Mb or more:
    libs  94.6Mb
GNU make is a SystemRequirements.
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb
GNU make is a SystemRequirements.
installed size is 49.0Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib   34.2Mb
    libs  11.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    external   1.6Mb
    libs       3.8Mb
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Specified C++11: please drop specification unless essential
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    swipl  26.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.8Mb
    help   2.4Mb
'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   5.0Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    rmarkdown  11.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Gviz’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs       2.3Mb
    projects   2.9Mb
Specified C++11: please drop specification unless essential
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 116.0Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    libs  114.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.0Mb
Specified C++11: please drop specification unless essential
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  21.2Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 216.3Mb
  sub-directories of 1Mb or more:
    data    1.5Mb
    libs  213.8Mb
GNU make is a SystemRequirements.
Running examples in ‘RtsEva-Ex.R’ failed
The error most likely occurred in:

> ### Name: tsEstimateAverageSeasonality
> ### Title: Estimate Average Seasonality
> ### Aliases: tsEstimateAverageSeasonality
> 
> ### ** Examples
> 
> timeAndSeries <- ArdecheStMartin
> timeStamps <- ArdecheStMartin[,1]
> series  <- ArdecheStMartin[,2]
> timeWindow <- 30*365  # 30 years
> rs <- tsEvaDetrendTimeSeries(timeStamps, series, timeWindow)
> nRunMn <- rs@nRunMn
> cat("computing trend seasonality ...\n")
computing trend seasonality ...
> seasonalitySeries <- rs@detrendSeries
> result <- tsEstimateAverageSeasonality(timeStamps, seasonalitySeries, timeWindow=rs@nRunMn)
Warning in pracma::interp1(avgTmStamp, monthAvgVec, timeStampsN, method = "spline") :
  Points in argument in 'x' unsorted; will be sorted.
Warning in pracma::interp1(avgTmStamp, monthAvgVex, timeStampsN, method = "spline") :
  Points in argument in 'x' unsorted; will be sorted.
> plot(result$regime, type = "l", xlab = "Day", ylab = "Regime", main = "Estimated Regime")
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot -> plot.default -> localWindow -> plot.window
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
'library' or 'require' calls in package code:
  ‘nimble’ ‘nimbleAPT’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmmADMB’
Package required but not available: ‘GSVAdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 48.4Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gpuR’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 64.2Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs     58.8Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    extdata   2.4Mb
Specified C++11: please drop specification unless essential
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Packages suggested but not available for checking:
  'BiocPkgTools', 'biocViews'
Packages unavailable to check Rd xrefs: ‘BiocPkgTools’, ‘biocViews’
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 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    include   1.1Mb
    libs      5.8Mb
installed size is  8.9Mb
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    libs   8.5Mb
Specified C++11: please drop specification unless essential
installed size is 10.1Mb
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    libs    8.4Mb
    yacas   1.3Mb
Specified C++14: please drop specification unless essential
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs    9.1Mb
    yacas   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.1Mb
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    libs  16.0Mb
installed size is 11.2Mb
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Specified C++14: please drop specification unless essential
installed size is 36.9Mb
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checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
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    libs   8.2Mb
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
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'LazyData' is specified without a 'data' directory
installed size is 14.9Mb
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Specified C++11: please drop specification unless essential
installed size is 22.3Mb
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checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
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checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
installed size is 55.6Mb
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    R      2.1Mb
    libs  53.0Mb
Specified C++11: please drop specification unless essential
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   4.0Mb
Packages suggested but not available for checking:
  'GOstats', 'networkTomography', 'org.Sc.sgd.db'
'LazyData' is specified without a 'data' directory
installed size is 46.8Mb
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    libs  46.7Mb
'LazyData' is specified without a 'data' directory
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installed size is  5.3Mb
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installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  5.3Mb
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    bin   4.5Mb
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
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    doc    1.7Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
installed size is  6.3Mb
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    doc       5.1Mb
    extdata   1.1Mb
installed size is  7.4Mb
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    doc    3.9Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    libs   3.9Mb
installed size is  5.3Mb
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    data   2.0Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    data   2.7Mb
    doc    2.3Mb
installed size is  5.6Mb
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    libs   4.8Mb
Packages suggested but not available for checking:
  'dittoSeq', 'DropletUtils', 'Nebulosa'
Packages unavailable to check Rd xrefs: ‘DropletUtils’, ‘Nebulosa’
Package required but not available: ‘glmGamPoi’

Package suggested but not available for checking: ‘Linnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
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    data   3.2Mb
    libs   3.0Mb
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(scDHA)
  libtorch is not installed. Use `torch::install_torch()` to download and install libtorch
  > 
  > on_cran <- function() !identical(Sys.getenv("NOT_CRAN"), "true")
  > 
  > if((!torch::torch_is_installed()) & 
  +    (tolower(Sys.info()[["sysname"]]) != "windows") & 
  +    (!on_cran()))
  + {
  +   torch::install_torch()
  + }
  > 
  > Sys.setenv(IN_TEST_scDHA="true")
  > 
  > test_check("scDHA")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 3 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-scDHA.R:3:3', 'test-scDHA.R:41:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-scDHA.R:21:3'): scDHA.vis can run ──────────────────────────────
  Error in `irlba::irlba(L, nv = n, nu = 0, maxit = iters)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
      ▆
   1. └─scDHA::scDHA.vis(result, ncores = 2, seed = 1) at test-scDHA.R:21:3
   2.   └─uwot::umap(data, n_threads = ncores)
   3.     └─uwot:::uwot(...)
   4.       └─uwot:::spectral_init(V, ndim = n_components, verbose = verbose)
   5.         └─uwot:::irlba_tsvd_normalized_laplacian_init(A, ndim, verbose = FALSE)
   6.           └─uwot:::irlba_spectral_tsvd(L, ndim + 1)
   7.             ├─base::suppressWarnings(...)
   8.             │ └─base::withCallingHandlers(...)
   9.             └─irlba::irlba(L, nv = n, nu = 0, maxit = iters)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 3 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'ontoProc', 'rrvgo', 'SingleCellSignalR'
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Package required and available but unsuitable version: ‘UCell’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘batchelor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘simplifyEnrichment’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GSVA’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/scorematchingad.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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    libs   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'AUCell', 'decoupleR', 'infercnv', 'Nebulosa'
Package unavailable to check Rd xrefs: ‘infercnv’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmGamPoi’
installed size is 20.9Mb
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Package suggested but not available for checking: ‘oligoClasses’
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
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    libs   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sdcSpatial.Rmd’ using rmarkdown
Quitting from lines 190-192 (sdcSpatial.Rmd) 
Error: processing vignette 'sdcSpatial.Rmd' failed with diagnostics:
different crs
--- failed re-building ‘sdcSpatial.Rmd’

SUMMARY: processing the following file failed:
  ‘sdcSpatial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.3Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is 87.8Mb
  sub-directories of 1Mb or more:
    libs  85.9Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'MuSiC', 'seAMLessData'
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R   9.0Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  16.5Mb
GNU make is a SystemRequirements.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.4Mb
'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:
    data   2.9Mb
    libs   7.9Mb
Packages required but not available: 'ggmsa', 'msa'

Package suggested but not available for checking: ‘org.Rn.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rsbml’
Package suggested but not available for checking: ‘ArrayExpress’
Package unavailable to check Rd xrefs: ‘ArrayExpress’
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Error(s) in re-building vignettes:
  ...
--- re-building ‘SEI_vignette.Rnw’ using knitr
Error: processing vignette 'SEI_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'SEI_vignette.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SEI_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    www  34.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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    libs   5.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SemiCompRisks.ltx’ using tex
Error: processing vignette 'SemiCompRisks.ltx' failed with diagnostics:
Running 'texi2dvi' on 'SemiCompRisks.ltx' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm8): Font bbm8 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SemiCompRisks.ltx’

SUMMARY: processing the following file failed:
  ‘SemiCompRisks.ltx’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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    R      2.3Mb
    libs   2.6Mb
Specified C++11: please drop specification unless essential
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs    21.0Mb
    models   1.6Mb
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.5Mb
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.4Mb
Specified C++14: please drop specification unless essential
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Package suggested but not available for checking: ‘airway’
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pwalign’
installed size is  5.9Mb
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    libs   4.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 55.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  53.4Mb
GNU make is a SystemRequirements.
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
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
Packages suggested but not available for checking: 'HDF5Array', 'BPCells'
Packages suggested but not available for checking:
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installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 265.4Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    libs    258.9Mb
    sqlite    1.5Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
installed size is  6.4Mb
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    doc       1.7Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is  9.5Mb
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'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    tutorials   3.6Mb
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installed size is 21.1Mb
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    www  10.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    help      1.7Mb
Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.9Mb
Packages unavailable to check Rd xrefs: ‘motifmatchr’, ‘TFBSTools’, ‘chromVAR’
Package suggested but not available for checking: ‘rhdf5’
Package required but not available: ‘GSVA’

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
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.0Mb
    libs   2.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
GNU make is a SystemRequirements.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  12.8Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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    libs   2.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
Package suggested but not available for checking: ‘INLA’
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
installed size is 23.3Mb
  sub-directories of 1Mb or more:
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    libs  20.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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    libs   2.7Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   6.8Mb
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    extdata   1.2Mb
    libs      6.5Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
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Package which this enhances but not available for checking: ‘kmndirs’
installed size is  7.4Mb
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GNU make is a SystemRequirements.
installed size is 38.2Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 31.7Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
installed size is  5.1Mb
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
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checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
installed size is  7.2Mb
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Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘smm.Rnw’ using Sweave
Error: processing vignette 'smm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'smm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘smm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
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    libs   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.4Mb
    libs  10.6Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Package which this enhances but not available for checking: ‘Rmpi’
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.9Mb
Package required but not available: ‘GWASTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  5.9Mb
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    R     4.1Mb
    doc   1.1Mb
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      3.8Mb
    extdata   1.1Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.3Mb
    libs   9.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DropletUtils’
installed size is  5.9Mb
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    data   4.0Mb
    doc    1.0Mb
Package suggested but not available for checking: ‘gridlayout’
installed size is  5.4Mb
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    data   4.8Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    R      2.0Mb
    libs   2.4Mb
installed size is  8.2Mb
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    extdata   5.9Mb
    libs      2.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
installed size is  7.4Mb
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    R   5.7Mb
Package suggested but not available for checking: ‘NLMR’
'LazyData' is specified without a 'data' directory
installed size is 39.1Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs  34.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    java   1.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'SparseM.ontology':
  ‘as.matrix.csr’ ‘is.matrix.csr’ ‘is.matrix.csc’ ‘is.matrix.ssr’
  ‘is.matrix.ssc’ ‘is.matrix.coo’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/spaths.Rcheck/00install.out’ for details.
Package required but not available: ‘SpatialExperiment’

Package suggested but not available for checking: ‘HDF5Array’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
installed size is 95.1Mb
  sub-directories of 1Mb or more:
    libs  94.2Mb
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.2Mb
Specified C++14: please drop specification unless essential
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  11.5Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.1Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
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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  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs  10.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Package suggested but not available for checking: ‘spDataLarge’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
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    shapes   5.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    help   1.5Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘scRNAseq’
Running examples in ‘speaq-Ex.R’ failed
The error most likely occurred in:

> ### Name: BWR
> ### Title: BW ratio calculation
> ### Aliases: BWR
> 
> ### ** Examples
> 
> res=makeSimulatedData();
> X=res$data;
> groupLabel=res$label;
> peakList <- detectSpecPeaks(X,
+                             nDivRange = c(128),
+                             scales = seq(1, 16, 2),
+                             baselineThresh = 50000,
+                             SNR.Th = -1,
+                             verbose=FALSE
+ );
> resFindRef<- findRef(peakList);
> refInd <- resFindRef$refInd;
> maxShift = 50;
> Y <- dohCluster(X,
+                 peakList = peakList,
+                 refInd = refInd,
+                 maxShift  = maxShift,
+                 acceptLostPeak = TRUE, verbose=FALSE);
Warning in min(peakList) :
  no non-missing arguments to min; returning Inf
Warning in max(peakList) :
  no non-missing arguments to max; returning -Inf
Error in startP:(minpeakList - 1) : result would be too long a vector
Calls: dohCluster -> .withMaxShift -> hClustAlign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘classic_speaq_vignette.Rmd’ using rmarkdown
Quitting from lines 111-120 (classic_speaq_vignette.Rmd) 
Error: processing vignette 'classic_speaq_vignette.Rmd' failed with diagnostics:
result would be too long a vector
--- failed re-building ‘classic_speaq_vignette.Rmd’

--- re-building ‘speaq2_illustrations.Rmd’ using rmarkdown
Quitting from lines 71-83 (speaq2_illustrations.Rmd) 
Error: processing vignette 'speaq2_illustrations.Rmd' failed with diagnostics:
invalid 'times' argument
--- failed re-building ‘speaq2_illustrations.Rmd’

SUMMARY: processing the following files failed:
  ‘classic_speaq_vignette.Rmd’ ‘speaq2_illustrations.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Undocumented S4 methods:
  generic '[' and siglist 'SpectraInTime,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTime,missing,ANY,ANY'
  generic '[' and siglist 'SpectraInTime,missing,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,ANY,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,missing,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Specified C++11: please drop specification unless essential
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.8Mb
    doc    1.5Mb
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is 52.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  50.5Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    help   1.1Mb
    libs  10.9Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs  40.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 104.3Mb
  sub-directories of 1Mb or more:
    libs  103.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Error(s) in re-building vignettes:
--- re-building ‘sstvars-vignette.Rnw’ using Sweave
Error: processing vignette 'sstvars-vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sstvars-vignette.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'sstvars-vignette.Rnw'

SUMMARY: processing the following file failed:
  'sstvars-vignette.Rnw'

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
installed size is 50.3Mb
  sub-directories of 1Mb or more:
    libs  50.0Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  11.7Mb
    lib       3.3Mb
GNU make is a SystemRequirements.
installed size is 90.0Mb
  sub-directories of 1Mb or more:
    libs  89.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Package suggested but not available for checking: ‘snpStats’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   5.1Mb
Package unavailable to check Rd xrefs: ‘snpStats’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      4.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.3Mb
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
installed size is 62.7Mb
  sub-directories of 1Mb or more:
    libs  61.5Mb
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.4Mb
Specified C++11: please drop specification unless essential
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.9Mb
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:
    libs   7.1Mb
installed size is 10.4Mb
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Malformed Title field: should not end in a period.
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efpFunctional: multiple local function definitions for ‘plotProcess’
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mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
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Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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    Amendments to functions
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Problems with news in ‘NEWS.md’:
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    pre-release switchboard (2020 - 2021)
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
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checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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installed size is 33.8Mb
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GNU make is a SystemRequirements.
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/terra.Rcheck/00install.out’ for details.
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Problems with news in ‘NEWS.md’:
No news entries found.
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GNU make is a SystemRequirements.
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checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
No news entries found.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
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Package unavailable to check Rd xrefs: ‘Rblpapi’
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installed size is 46.4Mb
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Running ‘testthat.R’ [9s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidystats)
  This version of tidystats uses a new and improved way of structuring statistics. This breaks previous (major) versions of tidystats.
  > 
  > test_check("tidystats")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_glm.R:118:3'): glm anova works ───────────────────────────────
  `tidy_model` not equal to `expected_tidy_model`.
  Component "groups": Component 1: Component 2: Component 2: Component 2: Length mismatch: comparison on first 4 components
  Component "groups": Component 1: Component 2: Component 3: Component 2: Length mismatch: comparison on first 4 components
  Backtrace:
      ▆
   1. └─tidystats:::expect_equal_models(model = model, expected_tidy_model = expected_statistics$anova_glm) at test_glm.R:118:3
   2.   └─testthat::expect_equal(tidy_model, expected_tidy_model, tolerance = tolerance)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  Error: Test failures
  Execution halted
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checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
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No news entries found.
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GNU make is a SystemRequirements.
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installed size is 16.6Mb
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installed size is 29.1Mb
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GNU make is a SystemRequirements.
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installed size is  6.1Mb
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installed size is 211.9Mb
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No news entries found.
installed size is 13.0Mb
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installed size is  8.8Mb
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Packages required but not available: 'csaw', 'HiCDOC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is  5.9Mb
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installed size is  8.6Mb
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installed size is  6.1Mb
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installed size is 17.6Mb
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Package required but not available: ‘snpStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
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'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/triptych.Rcheck/00install.out’ for details.
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Malformed Title field: should not end in a period.
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installed size is 33.6Mb
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GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.9Mb
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

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

Error: Vignette re-building failed.
Execution halted
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'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 46.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 138.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 15.4Mb
  sub-directories of 1Mb or more:
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    libs  12.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.6Mb
  sub-directories of 1Mb or more:
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    libs   2.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 96.8Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  7.2Mb
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installed size is 128.9Mb
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GNU make is a SystemRequirements.
installed size is 22.2Mb
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    libs  21.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data       1.1Mb
    doc        1.4Mb
    shinyapp   4.9Mb
Specified C++11: please drop specification unless essential
installed size is 27.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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    help   4.4Mb
installed size is  5.5Mb
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    help   2.6Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Specified C++14: please drop specification unless essential
installed size is 14.8Mb
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    libs  13.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 65.7Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘USA.state.boundaries.data’
installed size is  7.2Mb
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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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
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checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
installed size is  7.1Mb
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'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
installed size is 14.0Mb
  sub-directories of 1Mb or more:
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Running ‘testthat.R’ [39s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(uwot)
  Loading required package: Matrix
  > 
  > test_check("uwot")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 683 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_normlaplacian.R:36:5'): normalized laplacian ───────────────────
  Error in `irlba::irlba(L, nv = n, nu = 0, maxit = iters)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
      ▆
   1. └─uwot:::irlba_tsvd_normalized_laplacian_init(sparse_m) at test_normlaplacian.R:36:5
   2.   └─uwot:::irlba_spectral_tsvd(L, ndim + 1)
   3.     ├─base::suppressWarnings(...)
   4.     │ └─base::withCallingHandlers(...)
   5.     └─irlba::irlba(L, nv = n, nu = 0, maxit = iters)
  ── Error ('test_output.R:315:3'): (code run outside of `test_that()`) ──────────
  Error in `irlba::irlba(L, nv = n, nu = 0, maxit = iters)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
      ▆
   1. └─uwot::umap(...) at test_output.R:315:3
   2.   └─uwot:::uwot(...)
   3.     └─uwot:::spectral_init(...)
   4.       └─uwot:::irlba_tsvd_normalized_laplacian_init(A, ndim, verbose = FALSE)
   5.         └─uwot:::irlba_spectral_tsvd(L, ndim + 1)
   6.           ├─base::suppressWarnings(...)
   7.           │ └─base::withCallingHandlers(...)
   8.           └─irlba::irlba(L, nv = n, nu = 0, maxit = iters)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 683 ]
  Error: Test failures
  Execution halted
installed size is 49.7Mb
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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  9.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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installed size is 250.9Mb
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'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:
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   7.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
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checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  49.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.3Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
GNU make is a SystemRequirements.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     30.0Mb
GNU make is a SystemRequirements.
installed size is 62.1Mb
  sub-directories of 1Mb or more:
    libs  61.7Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
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installed size is  9.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 115.7Mb
  sub-directories of 1Mb or more:
    libs  114.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘prepr’
Problems with news in ‘NEWS.md’:
No news entries found.
Error(s) in re-building vignettes:
--- re-building ‘use_case.Rmd’ using rmarkdown
--- finished re-building ‘use_case.Rmd’

--- re-building ‘weatherOz.Rmd’ using rmarkdown_notangle
--- finished re-building ‘weatherOz.Rmd’

--- re-building ‘weatherOz_for_BOM.Rmd’ using rmarkdown_notangle
--- finished re-building ‘weatherOz_for_BOM.Rmd’

--- re-building ‘weatherOz_for_DPIRD.Rmd’ using rmarkdown_notangle
File vignettes/view_sw_ag_region-1.png not found in resource path
Error: processing vignette 'weatherOz_for_DPIRD.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘weatherOz_for_DPIRD.Rmd’

--- re-building ‘weatherOz_for_SILO.Rmd’ using rmarkdown_notangle
--- finished re-building ‘weatherOz_for_SILO.Rmd’

SUMMARY: processing the following file failed:
  ‘weatherOz_for_DPIRD.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.5Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
installed size is 92.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs  87.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 57.4Mb
  sub-directories of 1Mb or more:
    libs  57.0Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: ‘wordnetDicts’
Error(s) in re-building vignettes:
--- re-building ‘features.Rmd’ using rmarkdown
--- finished re-building ‘features.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Error reading bibliography file references.bib:
(line 56, column 16):
unexpected 't'
Error: processing vignette 'overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 25
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
Package suggested but not available for checking: ‘wmtsa’
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘ROTS’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    help   1.9Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  12.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 54.1Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    java  30.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
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installed size is 25.2Mb
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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
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 45.0Mb
  sub-directories of 1Mb or more:
    libs  44.7Mb
GNU make is a SystemRequirements.
installed size is 43.1Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   4.6Mb
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 40.6Mb
  sub-directories of 1Mb or more:
    libs  40.1Mb
GNU make is a SystemRequirements.
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: \_
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Specified C++11: please drop specification unless essential
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    libs  29.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is 107.4Mb
  sub-directories of 1Mb or more:
    libs  106.4Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   2.9Mb
    libs      8.8Mb
'LazyData' is specified without a 'data' directory
installed size is 13.4Mb
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installed size is  7.6Mb
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'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
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installed size is 14.4Mb
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installed size is 151.8Mb
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installed size is 10.4Mb
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installed size is  5.1Mb
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installed size is  6.2Mb
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Package suggested but not available for checking: ‘HiTC’
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'LazyData' is specified without a 'data' directory
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installed size is  5.7Mb
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Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘epiR’
Package which this enhances but not available for checking: ‘asreml’
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'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘tripack’
Package unavailable to check Rd xrefs: ‘tripack’
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installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
Bad \usage lines found in documentation object 'annmatrix':
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  <unescaped bksl>method{@}{annmatrix}(object, name) <- value

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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installed size is 35.6Mb
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Package suggested but not available for checking: ‘competitiontoolbox’
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sort_asap: no visible global function definition for ‘sort_by’
Undefined global functions or variables:
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Package suggested but not available for checking: ‘ArchaeoData’
Found the following significant warnings:
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  Warning: read_chronomodel.Rd:36: unknown macro '\abbr'
  Warning: read_oxcal.Rd:27: unknown macro '\abbr'
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/ArchaeoPhases.Rcheck/00install.out’ for details.
prepare_Rd: read_bcal.Rd:27: unknown macro '\abbr'
prepare_Rd: read_chronomodel.Rd:36: unknown macro '\abbr'
prepare_Rd: read_oxcal.Rd:27: unknown macro '\abbr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  8.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
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Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Package suggested but not available for checking: ‘GLAD’
Packages suggested but not available for checking:
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Package unavailable to check Rd xrefs: ‘GLAD’
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Specified C++11: please drop specification unless essential
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installed size is  6.6Mb
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installed size is 10.9Mb
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Package which this enhances but not available for checking: ‘asreml’
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GNU make is a SystemRequirements.
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installed size is 10.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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installed size is 97.8Mb
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Specified C++11: please drop specification unless essential
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checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
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installed size is  5.2Mb
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installed size is 67.1Mb
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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installed size is  8.5Mb
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GNU make is a SystemRequirements.
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'library' or 'require' call not declared from: ‘x’
installed size is 24.8Mb
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installed size is  6.3Mb
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checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
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GNU make is a SystemRequirements.
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Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘BRugs’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 100.0Mb
  sub-directories of 1Mb or more:
    libs  98.5Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is 66.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  63.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
'LazyData' is specified without a 'data' directory
installed size is 56.1Mb
  sub-directories of 1Mb or more:
    libs  55.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    libs  36.6Mb
GNU make is a SystemRequirements.
installed size is 53.6Mb
  sub-directories of 1Mb or more:
    libs  53.0Mb
GNU make is a SystemRequirements.
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    libs  24.7Mb
Package which this enhances but not available for checking: ‘caret’
Specified C++11: please drop specification unless essential
installed size is 55.8Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  52.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    help   1.1Mb
    libs   7.8Mb
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
installed size is 10.9Mb
  sub-directories of 1Mb or more:
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    libs   6.5Mb
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
installed size is 167.4Mb
  sub-directories of 1Mb or more:
    include  167.3Mb
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
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installed size is  8.5Mb
  sub-directories of 1Mb or more:
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    libs   6.2Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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Specified C++14: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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    libs      2.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      8.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Specified C++11: please drop specification unless essential
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  16.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is 87.6Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   2.9Mb
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 20.5Mb
  sub-directories of 1Mb or more:
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    libs  17.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
installed size is  5.3Mb
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installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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installed size is  8.2Mb
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    libs      2.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Package listed in more than one of Depends, Imports, Suggests, Enhances:
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A package should be listed in only one of these fields.
Packages in Depends field not imported from:
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  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
checkRd: (-1) FighterAircraft.Rd:32: Escaped LaTeX specials: \&
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
installed size is 49.3Mb
  sub-directories of 1Mb or more:
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    libs     46.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘Seurat’
Package suggested but not available for checking: ‘IHW’
installed size is 45.6Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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Found the following significant warnings:

  Warning: 'blandr.output.text' is deprecated.
  Warning: 'blandr.output.text' is deprecated.
  Warning: 'blandr.output.text' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 162.1Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
installed size is  7.5Mb
  sub-directories of 1Mb or more:
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installed size is  7.7Mb
  sub-directories of 1Mb or more:
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    libs   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 33.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘reldist’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 177.5Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 91.8Mb
  sub-directories of 1Mb or more:
    libs  91.2Mb
GNU make is a SystemRequirements.
installed size is 51.8Mb
  sub-directories of 1Mb or more:
    libs  51.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 93.3Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.7Mb
Specified C++11: please drop specification unless essential
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
Packages suggested but not available for checking:
  'adiposerefdata', 'musclerefdata'
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Error(s) in re-building vignettes:
  ...
--- re-building ‘BonEV.Rnw’ using Sweave
Error: processing vignette 'BonEV.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'BonEV.tex' failed.
LaTeX errors:
! LaTeX Error: File `underscore.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \parindent
               0in^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘BonEV.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
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    libs   1.3Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is 394.8Mb
  sub-directories of 1Mb or more:
    include   10.3Mb
    lib      384.1Mb
GNU make is a SystemRequirements.
installed size is 93.4Mb
  sub-directories of 1Mb or more:
    libs  92.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘sparsenet’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.0Mb
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checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
installed size is 53.6Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 46.5Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'BayesFactor', 'rstan', 'rstanarm', 'MCMCpack'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘cmdstanr’
installed size is  9.2Mb
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Error(s) in re-building vignettes:
--- re-building ‘Brobdingnag.Rnw’ using Sweave
Loading required package: Brobdingnag
Loading required package: Matrix

Attaching package: ‘Brobdingnag’

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

    diag, t

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

    diag, t

Error: processing vignette 'Brobdingnag.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Brobdingnag.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Brobdingnag.Rnw’

--- re-building ‘S4_brob.Rnw’ using Sweave
Creating a new generic function for ‘max’ in the global environment
Creating a new generic function for ‘min’ in the global environment
Creating a new generic function for ‘range’ in the global environment
Creating a new generic function for ‘prod’ in the global environment
Creating a new generic function for ‘sum’ in the global environment
Error: processing vignette 'S4_brob.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'S4_brob.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘S4_brob.Rnw’

SUMMARY: processing the following files failed:
  ‘Brobdingnag.Rnw’ ‘S4_brob.Rnw’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘glmmADMB’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    components   1.0Mb
    fonts        2.8Mb
    lib          5.2Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs  27.7Mb
'LazyData' is specified without a 'data' directory
installed size is 110.2Mb
  sub-directories of 1Mb or more:
    libs  109.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
'LazyData' is specified without a 'data' directory
installed size is 177.1Mb
  sub-directories of 1Mb or more:
    libs  176.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Package suggested but not available for checking: ‘gsl’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘org.Mm.eg.db’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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    extdata   3.4Mb
pairwise.matrix: no visible global function definition for ‘%||%’
Undefined global functions or variables:
  %||%
Running examples in ‘bullseye-Ex.R’ failed
The error most likely occurred in:

> ### Name: pair_ace
> ### Title: Alternating conditional expectations correlation
> ### Aliases: pair_ace
> 
> ### ** Examples
> 
>  pair_ace(iris)
Error in rownames(m) %||% paste0("V", seq_along(xindex)) : 
  could not find function "%||%"
Calls: pair_ace -> pairwise -> pairwise.data.frame -> pairwise.matrix
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘calc_pairwise.Rmd’ using rmarkdown

Quitting from lines 44-46 [unnamed-chunk-3] (calc_pairwise.Rmd)
Error: processing vignette 'calc_pairwise.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building ‘calc_pairwise.Rmd’

--- re-building ‘integrating.Rmd’ using rmarkdown

Quitting from lines 57-62 [corrplot_assoc] (integrating.Rmd)
Error: processing vignette 'integrating.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building ‘integrating.Rmd’

--- re-building ‘vis_pairwise.Rmd’ using rmarkdown

Quitting from lines 52-53 [unnamed-chunk-3] (vis_pairwise.Rmd)
Error: processing vignette 'vis_pairwise.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building ‘vis_pairwise.Rmd’

SUMMARY: processing the following files failed:
  ‘calc_pairwise.Rmd’ ‘integrating.Rmd’ ‘vis_pairwise.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
'LazyData' is specified without a 'data' directory
installed size is 153.9Mb
  sub-directories of 1Mb or more:
    libs  151.8Mb
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘doMPI’
Specified C++11: please drop specification unless essential
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 131.7Mb
  sub-directories of 1Mb or more:
    libs  131.3Mb
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    libs  40.8Mb
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data  10.1Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ProFAST’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    libs  67.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
'LazyData' is specified without a 'data' directory
Packages required but not available: 'org.Dr.eg.db', 'org.Mm.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.1Mb
Package suggested but not available for checking: ‘batchelor’
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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    virtual_patient_simulator   3.1Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.9Mb
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    libs  35.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    www  12.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  19.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc  19.9Mb
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   3.5Mb
installed size is 54.8Mb
  sub-directories of 1Mb or more:
    libs  53.8Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Specified C++11: please drop specification unless essential
installed size is  6.4Mb
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'LazyData' is specified without a 'data' directory
installed size is 149.7Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 17.9Mb
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installed size is 22.2Mb
  sub-directories of 1Mb or more:
    doc   16.4Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.6Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘mirt’
installed size is  6.1Mb
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    libs   3.2Mb
Package unavailable to check Rd xrefs: ‘mirt’
installed size is  5.9Mb
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    data   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is 15.4Mb
  sub-directories of 1Mb or more:
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    doc    2.0Mb
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Error(s) in re-building vignettes:
--- re-building ‘cem.Rnw’ using Sweave
Loading required package: cem
Loading required package: tcltk
Loading required package: lattice

How to use CEM? Type vignette("cem")

Loading required package: Amelia
Loading required package: Rcpp
## 
## Amelia II: Multiple Imputation
## (Version 1.8.1, built: 2022-11-18)
## Copyright (C) 2005-2023 James Honaker, Gary King and Matthew Blackwell
## Refer to http://gking.harvard.edu/amelia/ for more information
## 
Error: processing vignette 'cem.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cem.tex' failed.
BibTeX errors:
The top-level auxiliary file: cem.aux
I couldn't open style file apsr.bst
---line 66 of file cem.aux
 : \bibstyle{apsr
 :               }
I'm skipping whatever remains of this command
I found no style file---while reading file cem.aux
--- failed re-building ‘cem.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.5Mb
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Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘linkcomm’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
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    include  37.8Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
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    R     5.0Mb
    doc   3.2Mb
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘darts’
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Package suggested but not available for checking: ‘countreg’
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Packages suggested but not available for checking: 'drc', 'qpcR'
Package unavailable to check Rd xrefs: ‘qpcR’
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Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
installed size is  5.5Mb
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    help   2.2Mb
installed size is 18.0Mb
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'entab', 'mzR'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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installed size is  8.0Mb
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Note: skipping ‘CIARA.Rmd’ due to unavailable dependencies: 'Seurat'
'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
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'LazyData' is specified without a 'data' directory
Packages required but not available:
  'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘userfriendlyscience’
installed size is  6.9Mb
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    libs   3.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
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    data   1.1Mb
    doc    3.5Mb
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installed size is 10.8Mb
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'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
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    libs   9.5Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pwalign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
Package suggested but not available for checking: ‘seqHMM’
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
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    data   3.4Mb
    doc    1.8Mb
installed size is 48.6Mb
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installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
installed size is 17.7Mb
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    libs  15.8Mb
installed size is 32.7Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘cloudUtil.Rnw’ using Sweave
Error: processing vignette 'cloudUtil.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cloudUtil.tex' failed.
LaTeX errors:
! LaTeX Error: File `pstricks.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cloudUtil.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.0Mb
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    libs  11.7Mb
Error(s) in re-building vignettes:
--- re-building ‘createStreams.Rmd’ using knitr
--- finished re-building ‘createStreams.Rmd’

--- re-building ‘fisher.sim.Rmd’ using knitr
--- finished re-building ‘fisher.sim.Rmd’

--- re-building ‘random_numbers.Rmd’ using knitr

Quitting from lines 63-96 [rnormGpu] (random_numbers.Rmd)
Error: processing vignette 'random_numbers.Rmd' failed with diagnostics:
ViennaCL: FATAL ERROR: CL_INVALID_PROGRAM_EXECUTABLE.
If you think that this is a bug in ViennaCL, please report it at viennacl-support@lists.sourceforge.net and supply at least the following information:
 * Operating System
 * Which OpenCL implementation (AMD, NVIDIA, etc.)
 * ViennaCL version
Many thanks in advance!
--- failed re-building ‘random_numbers.Rmd’

SUMMARY: processing the following file failed:
  ‘random_numbers.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
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    libs   8.3Mb
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is 85.6Mb
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installed size is 19.4Mb
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    libs  19.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘moe430a.db’
Error(s) in re-building vignettes:
--- re-building ‘clValid.Rnw’ using Sweave
Loading required package: cluster
Read 7 items

Attaching package: ‘BiocGenerics’

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

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

    I, expand.grid, unname

Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’

Loading required package: RankAggreg
Error: processing vignette 'clValid.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.28 \usepackage
                [mathcal]{euscript}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘clValid.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 17.1Mb
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    libs  15.4Mb
installed size is  6.2Mb
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    data   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘weight_cause_cox.rnw’ using Sweave
Error: processing vignette 'weight_cause_cox.rnw' failed with diagnostics:
Running 'texi2dvi' on 'weight_cause_cox.tex' failed.
LaTeX errors:
! LaTeX Error: File `pgfplots.sty' not found.

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

! Emergency stop.
<read *> 
         
l.28 \pgfplotsset
                 {compat=1.10}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘weight_cause_cox.rnw’

SUMMARY: processing the following file failed:
  ‘weight_cause_cox.rnw’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
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Package suggested but not available for checking: ‘tobit1’
Error(s) in re-building vignettes:
--- re-building ‘cmvnorm.Rnw’ using Sweave

Attaching package: ‘cmvnorm’

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

    sd, var


Attaching package: ‘elliptic’

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

    Im<-, Re<-, sd

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

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Error: processing vignette 'cmvnorm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cmvnorm.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cmvnorm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  5.2Mb
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    extdata   1.7Mb
Package suggested but not available for checking: ‘PopGenome’
installed size is  6.2Mb
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    R      2.0Mb
    libs   3.6Mb
Package suggested but not available for checking: ‘disttree’
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘wTO’
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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    libs   5.6Mb
Package suggested but not available for checking: ‘car’
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  5.7Mb
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    doc    3.5Mb
    help   1.9Mb
installed size is 10.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.9Mb
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    R      1.1Mb
    libs  12.9Mb
installed size is  5.4Mb
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    data   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    doc   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    doc       2.4Mb
    extdata   2.1Mb
installed size is 67.6Mb
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    libs  66.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 16.4Mb
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    libs  14.4Mb
installed size is  7.0Mb
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Specified C++11: please drop specification unless essential
installed size is  5.3Mb
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    libs   4.7Mb
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'pcalg', 'InvariantCausalPrediction', 'backShift', 'CAM', 'mboost',
  'huge', 'flare'
Running examples in ‘CompareMultipleModels-Ex.R’ failed
The error most likely occurred in:

> ### Name: best_model_finder
> ### Title: Finding the Best Model Using Eight Metrics Values
> ### Aliases: best_model_finder
> 
> ### ** Examples
> 
> set.seed(123) # for reproducibility
> Y <- rnorm(100, 100, 10)
> model_1 <-CEEMDANML::carigaan(Y, ratio = 0.8, n_lag = 4)
Error in optim(init[mask], armafn, method = optim.method, hessian = TRUE,  : 
  non-finite finite-difference value [1]
Calls: <Anonymous> -> arima -> optim
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘compare-intro.Rnw’ using Sweave
Error: processing vignette 'compare-intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'compare-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {hyperref} % for \url^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘compare-intro.Rnw’

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

Attaching package: ‘compare’

The following object is masked from ‘package:base’:

    isTRUE

--- finished re-building ‘fundamentals.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 28.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'scagnostics', 'parsnip', 'C50', 'bartMachine', 'caret'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.9Mb
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    libs  10.4Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'conosPanel', 'org.Mm.eg.db', 'p2data', 'rhdf5'
installed size is 11.3Mb
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    libs   9.6Mb
installed size is 20.6Mb
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    libs  20.4Mb
installed size is  6.4Mb
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    doc   5.4Mb
installed size is 70.2Mb
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    libs  68.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘org.Mm.eg.db’

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
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
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    vignette_data   2.6Mb
installed size is  6.1Mb
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    libs   2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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    help   2.6Mb
    libs   3.1Mb
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs          2.9Mb
    sample_data   2.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘phyloseq’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProData’
Package suggested but not available for checking: ‘xcms’
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
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    extdata  17.7Mb
installed size is  7.2Mb
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checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
installed size is  7.2Mb
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    data   4.7Mb
    doc    1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.5Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.9Mb
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
installed size is 62.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  60.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.9Mb
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.2Mb
    libs   5.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 41.6Mb
  sub-directories of 1Mb or more:
    libs  41.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’
'LazyData' is specified without a 'data' directory
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc   11.7Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    doc    1.6Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
'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: ‘ctmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 180.8Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    data    2.0Mb
    libs  175.5Mb
GNU make is a SystemRequirements.
Running ‘testthat.R’ [73s/114s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Chain 1: Iteration: 290 / 300 [ 96%]  (Sampling)
  Chain 2: Iteration: 190 / 300 [ 63%]  (Sampling)
  Chain 1: Iteration: 300 / 300 [100%]  (Sampling)
  Chain 1: 
  Chain 1:  Elapsed Time: 22.012 seconds (Warm-up)
  Chain 1:                17.161 seconds (Sampling)
  Chain 1:                39.173 seconds (Total)
  Chain 1: 
  Chain 2: Iteration: 210 / 300 [ 70%]  (Sampling)
  Chain 2: Iteration: 230 / 300 [ 76%]  (Sampling)
  Chain 2: Iteration: 250 / 300 [ 83%]  (Sampling)
  Chain 2: Iteration: 270 / 300 [ 90%]  (Sampling)
  Chain 2: Iteration: 290 / 300 [ 96%]  (Sampling)
  
  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
Package which this enhances but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘TCGAbiolinks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required and available but unsuitable versions:
  'stats', 'tools', 'utils'

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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    libs  38.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    doc    1.2Mb
    help   1.1Mb
    libs   4.7Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    docs          1.0Mb
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.1Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: jpegReport.Rd:22: unknown macro '\abbr'
  Warning: jpegReport.Rd:50: unknown macro '\abbr'
  Warning: jpegReport.Rd:53: unknown macro '\abbr'
  Warning: jpegReport.Rd:56: unknown macro '\abbr'
  Warning: jpegReport.Rd:58: unknown macro '\abbr'
  Warning: jpegReport.Rd:62: unknown macro '\abbr'
  Warning: pdfReport.Rd:101: unknown macro '\abbr'
  Warning: pngReport.Rd:22: unknown macro '\abbr'
  Warning: pngReport.Rd:50: unknown macro '\abbr'
  Warning: pngReport.Rd:53: unknown macro '\abbr'
  Warning: pngReport.Rd:55: unknown macro '\abbr'
  Warning: pngReport.Rd:59: unknown macro '\abbr'
  Warning: readReportTable.Rd:35: unknown macro '\abbr'
  Warning: readReportTable.Rd:167: unknown macro '\abbr'
  Warning: scanReport.Rd:45: unknown macro '\abbr'
  Warning: scanReport.Rd:60: unknown macro '\abbr'
  Warning: scanReport.Rd:61: unknown macro '\abbr'
  Warning: scanReport.Rd:162: unknown macro '\abbr'
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/D4TAlink.light.Rcheck/00install.out’ for details.
prepare_Rd: jpegReport.Rd:22: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:50: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:53: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:56: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:58: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:62: unknown macro '\abbr'
prepare_Rd: pdfReport.Rd:101: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:22: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:50: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:53: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:55: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:59: unknown macro '\abbr'
prepare_Rd: readReportTable.Rd:35: unknown macro '\abbr'
prepare_Rd: readReportTable.Rd:167: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:45: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:60: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:61: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:162: unknown macro '\abbr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   4.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
LazyData DB of 5.1 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   2.0Mb
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘DBR.Rnw’ using Sweave
DBR 1.4.1
Bayesian Discretized Beta Regression for the Analysis of Ratings Data
Warning in cor.test.default(pain$severity, pain$interference, method = "spearman") :
  Cannot compute exact p-value with ties
Warning in cor.test.default(pain$age, pain$interference, method = "spearman") :
  Cannot compute exact p-value with ties
Warning in ks.test.default(pred_sample, pain$interference) :
  p-value will be approximate in the presence of ties
Error: processing vignette 'DBR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'DBR.tex' failed.
LaTeX errors:
! LaTeX Error: File `breqn.sty' not found.

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

! Emergency stop.
<read *> 
         
l.18 \usepackage
                {atbegshi}% http://ctan.org/pkg/atbegshi^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘DBR.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.5Mb
Package required but not available: ‘dada2’

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

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
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘BRugs’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    libs  50.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.3Mb
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  22.4Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'EMD', 'astrochron'
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   2.2Mb
    libs  12.9Mb
Package suggested but not available for checking: ‘missMDA’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  33.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package suggested but not available for checking: ‘Rdonlp2’
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.N’ ‘.Nmiss’ ‘.Q1’ ‘.Q3’ ‘.factorN’ ‘.factorNmiss’ ‘.factorQ1’
  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
  ‘.factorsd’ ‘.max’ ‘.mean’ ‘.median’ ‘.min’ ‘.sd’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.8Mb
    help   2.5Mb
    libs   3.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Package suggested but not available for checking: ‘OSAT’
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Error(s) in re-building vignettes:
  ...
--- re-building ‘desirability.Rnw’ using Sweave
Error: processing vignette 'desirability.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'desirability.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm2e.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘desirability.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'psych', 'sirt'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'signatureSearch', 'signatureSearchData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'IHW', 'RNASeqPower', 'zFPKM'
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  15.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'KrigInv', 'GPareto'
Package unavailable to check Rd xrefs: ‘KrigInv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'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  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘dirmcmc_vignette.Rnw’ using Sweave
Error: processing vignette 'dirmcmc_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'dirmcmc_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `todonotes.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘dirmcmc_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 48.1Mb
  sub-directories of 1Mb or more:
    libs  47.5Mb
installed size is 87.5Mb
  sub-directories of 1Mb or more:
    libs  86.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Package unavailable to check Rd xrefs: ‘airway’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
Package which this enhances but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [6s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 31 - 28 == 3
  ── Failure ('test-realized_duration.R:158:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 31 - 28 == 3
  ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 31 - 28 == 3
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Package suggested but not available for checking: ‘BOLTSSIRR’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
installed size is 51.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs  48.0Mb
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
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Error(s) in re-building vignettes:
--- re-building ‘dlsem_vignette.Rnw’ using Sweave
Loading required package: dlsem
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
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    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Rgraphviz
Loading required package: grid
Error: processing vignette 'dlsem_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'dlsem_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘dlsem_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
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GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
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Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Problems with news in ‘NEWS.md’:
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Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘doMPI’
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GNU make is a SystemRequirements.
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Package required but not available: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
installed size is 10.3Mb
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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The following files should probably not be installed:
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Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
installed size is 10.8Mb
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GNU make is a SystemRequirements.
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Error in load(p, envir = env) : empty (zero-byte) input file
  Calls: <Anonymous> ... suppressPackageStartupMessages -> withCallingHandlers -> load
  Execution halted
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
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GNU make is a SystemRequirements.
Package required but not available: ‘opGMMassessment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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GNU make is a SystemRequirements.
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Error(s) in re-building vignettes:
--- re-building ‘ellipticpaper.Rnw’ using Sweave

Attaching package: ‘elliptic’

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

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Error: processing vignette 'ellipticpaper.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'ellipticpaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘ellipticpaper.Rnw’

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

Attaching package: ‘elliptic’

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

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Error: processing vignette 'residuetheorem.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'residuetheorem.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘residuetheorem.Rnw’

SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted
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GNU make is a SystemRequirements.
Packages required but not available:
  'minfi', 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19',
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CInp2TS
> ### Title: Function to convert Constant Input to Time Series
> ### Aliases: CInp2TS
> ### Keywords: CInp2TS
> 
> ### ** Examples
> 
> library(EmiStatR)
> library(zoo)

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> data("qs_factor")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> 
> cinp.daily.file <- qs_factor
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
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Undefined global functions or variables:
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
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Package suggested but not available for checking: ‘INLA’
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checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
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Malformed Description field: should contain one or more complete sentences.
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checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘exuberdata’
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checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
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No news entries found.
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
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Running examples in ‘familial-Ex.R’ failed
The error most likely occurred in:

> ### Name: center.test
> ### Title: Center test
> ### Aliases: center.test
> 
> ### ** Examples
> 
> set.seed(123)
> 
> test <- center.test(MASS::galaxies, mu = 21000, nboot = 100)
> print(test)
-----------------------------------------------
familial test of centers with huber family
-----------------------------------------------
mu = 21000 
posterior probabilities: 
  H0   H1 
0.59 0.41 
optimal decision: indeterminate 
> plot(test)
Error in validObject(.Object) : 
  invalid class “FncBand” object: superclass "mMatrix" not defined in the environment of the object's class
Calls: plot ... initialize -> initialize -> initMatrix -> validObject
Execution halted
Running ‘testthat.R’ [75s/116s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(familial)
  > 
  > test_check("familial")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-center-test.R:27:3'): plot function returns a plot ─────────────
  Error in `validObject(.Object)`: invalid class "FncBand" object: superclass "mMatrix" not defined in the environment of the object's class
  Backtrace:
       ▆
    1. ├─testthat::expect_s3_class(plot(test), "ggplot") at test-center-test.R:27:3
    2. │ └─testthat::quasi_label(enquo(object), arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::plot(test)
    5. └─familial:::plot.center.test(test)
    6.   └─base::lapply(band, bands)
    7.     └─familial (local) FUN(X[[i]], ...)
    8.       ├─base::data.frame(...)
    9.       └─DepthProc::fncGetBand(DepthProc::fncDepth(boot.wide), level)
   10.         └─methods::new("FncBand", bands, index = obj@index, level = band)
   11.           ├─methods::initialize(value, ...)
   12.           └─methods::initialize(value, ...)
   13.             └─methods (local) initMatrix(.Object, ...)
   14.               └─methods::validObject(.Object)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 56-57 [unnamed-chunk-3] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
invalid class "FncBand" object: superclass "mMatrix" not defined in the environment of the object's class
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
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installed size is 11.9Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
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installed size is 18.3Mb
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installed size is 15.1Mb
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installed size is  7.3Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is 43.9Mb
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installed size is  6.7Mb
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installed size is 51.5Mb
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Package suggested but not available for checking: ‘coxKM’
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installed size is  5.8Mb
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installed size is  6.0Mb
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.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
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installed size is  6.7Mb
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installed size is  7.7Mb
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installed size is 10.2Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘DESeq2’
installed size is  5.9Mb
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installed size is 32.1Mb
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GNU make is a SystemRequirements.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/fcl.Rcheck/00install.out’ for details.
installed size is 10.9Mb
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installed size is  6.9Mb
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Package suggested but not available for checking: ‘fields’
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installed size is 14.3Mb
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GNU make is a SystemRequirements.
installed size is  5.0Mb
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installed size is 12.0Mb
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checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
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checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
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installed size is  5.9Mb
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Error(s) in re-building vignettes:
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--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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Package suggested but not available for checking: ‘gridlayout’
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Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
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installed size is 11.9Mb
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installed size is  7.8Mb
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installed size is  7.5Mb
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checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
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installed size is 315.7Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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Malformed Description field: should contain one or more complete sentences.
installed size is 26.5Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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Problems with news in ‘NEWS.md’:
No news entries found.
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Problems with news in ‘NEWS.md’:
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Package suggested but not available for checking: ‘RandomFields’
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Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
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--- re-building ‘lala2015frbs.ltx’ using tex
--- finished re-building ‘lala2015frbs.ltx’

--- re-building ‘lala2015pmml.Rtex’ using Sweave
Warning in mean.default((real.val - res.test)^2) :
  argument is not numeric or logical: returning NA
Error: processing vignette 'lala2015pmml.Rtex' failed with diagnostics:
Running 'texi2dvi' on 'lala2015pmml.tex' failed.
LaTeX errors:
! LaTeX Error: File `elsarticle.cls' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'lala2015pmml.Rtex'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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installed size is  6.7Mb
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Package suggested but not available for checking: ‘dggrids’
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Package suggested but not available for checking: ‘RTCGA.rnaseq’
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Error(s) in re-building vignettes:
--- re-building ‘gamboostLSS_Tutorial.Rnw’ using Sweave
Loading required package: R2BayesX
Loading required package: BayesXsrc
Loading required package: colorspace
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-42. For overview type 'help("mgcv-package")'.
Loading required package: gamboostLSS
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs

Attaching package: 'gamboostLSS'

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

    model.weights

Loading required namespace: BayesX
Error: processing vignette 'gamboostLSS_Tutorial.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'gamboostLSS_Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.18 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'gamboostLSS_Tutorial.Rnw'

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

Error: Vignette re-building failed.
Execution halted
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Package suggested but not available for checking: ‘caret’
Package which this enhances but not available for checking: ‘doMPI’
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GNU make is a SystemRequirements.
installed size is 60.6Mb
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installed size is 16.7Mb
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GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
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No news entries found.
Package which this enhances but not available for checking: ‘simplifyEnrichment’
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Package required but not available: ‘reactome.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/GeoModels.Rcheck/00install.out’ for details.
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘RandomFields’

Package which this enhances but not available for checking: ‘INLA’
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
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Package suggested but not available for checking: ‘RGtk2’
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Package required but not available: ‘ggmsa’

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

> ### Name: Cardiological
> ### Title: Cardiological data example
> ### Aliases: Cardiological
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Cardiological)
> ggInterval_index(Cardiological, aes(x = Syst))
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'tbl_subset_col' not found
Calls: ggInterval_index ... as.data.frame -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggESDA.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 47-57 (ggESDA.Rmd) 
Error: processing vignette 'ggESDA.Rmd' failed with diagnostics:
object 'tbl_subset_col' not found
--- failed re-building ‘ggESDA.Rmd’

SUMMARY: processing the following file failed:
  ‘ggESDA.Rmd’

Error: Vignette re-building failed.
Execution halted
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installed size is 11.0Mb
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Packages suggested but not available for checking:
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checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
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checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': ‘scales:::censor’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘productplots:::bound’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
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GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'psych', 'psychTools'
installed size is  5.8Mb
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No news entries found.
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  'BSgenome.Hsapiens.UCSC.hg19.masked'
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checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
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checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
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checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
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Malformed Description field: should contain one or more complete sentences.
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Running examples in ‘gluvarpro-Ex.R’ failed
The error most likely occurred in:

> ### Name: preprocessgvp
> ### Title: preprocessing raw data from continuous glucose monitoring
> ### Aliases: preprocessgvp
> 
> ### ** Examples
> 
> data("datagvp4")
> preprocessgvp(datagvp4)
Error in preprocessgvp(datagvp4) : 
  Variable date and time must have yyyy/mm/dd and hh:mm:ss format.
Execution halted
Package unavailable to check Rd xrefs: ‘caret’
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘SeqVarTools’
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Problems with news in ‘NEWS.md’:
No news entries found.
Package unavailable to check Rd xrefs: ‘repeated’
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Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'Overview.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
pandoc: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/governor.Rcheck/vign_test/governor/vignettes/Overview.html: withFile: resource exhausted (No space left on device)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following file failed:
  ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
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Running ‘testthat.R’ [6s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 1. Failure ('test_predict.GP.R:64:9'): check predict.GP ─────────────────────
  smse2 >= 0 & smse2 < 30 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── 2. Failure ('test_predict.GP.R:81:9'): check predict.GP ─────────────────────
  sum(gpp2$complete_data[, 5] - ms2 < 1e-05) >= 10 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted
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Error(s) in re-building vignettes:
--- re-building ‘gplm-examples.Rnw’ using Sweave
Loading required package: AER
Loading required package: car
Loading required package: carData
Loading required package: lmtest
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: survival
Error: processing vignette 'gplm-examples.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'gplm-examples.tex' failed.
LaTeX errors:
! LaTeX Error: File `wasysym.sty' not found.

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

! Emergency stop.
<read *> 
         
l.20 \usepackage
                {comment}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘gplm-examples.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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Error(s) in re-building vignettes:
--- re-building ‘custom_ocl_gpuR.Rnw’ using knitr
Error: processing vignette 'custom_ocl_gpuR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'custom_ocl_gpuR.tex' failed.
LaTeX errors:
! Missing $ inserted.
<inserted text> 
                $
l.116 custom_
             ocl_gpuR.R\end{kframe}
! Emergency stop.
<inserted text> 
                $
l.116 custom_
             ocl_gpuR.R\end{kframe}
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘custom_ocl_gpuR.Rnw’

--- re-building ‘gpuR.Rnw’ using knitr
--- finished re-building ‘gpuR.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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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
Malformed Title field: should not end in a period.
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installed size is 15.2Mb
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Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
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Package required but not available: ‘EnsDb.Hsapiens.v75’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Package required but not available: ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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installed size is  6.0Mb
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Problems with news in ‘NEWS.md’:
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Packages unavailable to check Rd xrefs: ‘repeated’, ‘gnlm’
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checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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installed size is  8.2Mb
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There are ::: calls to the package's namespace in its code. A package
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Package required but not available: ‘handwriterRF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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GNU make is a SystemRequirements.
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installed size is 173.0Mb
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
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'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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installed size is 11.0Mb
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installed size is  7.6Mb
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Error(s) in re-building vignettes:
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--- re-building ‘HDXBoxeR.Rmd’ using rmarkdown
Error: processing vignette 'HDXBoxeR.Rmd' failed with diagnostics:
Error writing to connection:  No space left on device
--- failed re-building ‘HDXBoxeR.Rmd’

SUMMARY: processing the following file failed:
  ‘HDXBoxeR.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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installed size is  5.5Mb
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installed size is  6.3Mb
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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Specified C++11: please drop specification unless essential
installed size is  7.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
installed size is 24.4Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘geojsonio’
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installed size is  7.3Mb
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Specified C++11: please drop specification unless essential
installed size is  8.9Mb
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Package suggested but not available for checking: ‘INLA’
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Package suggested but not available for checking: ‘colorfulVennPlot’
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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installed size is 84.0Mb
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GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘HadoopStreaming’
installed size is  5.1Mb
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installed size is  7.8Mb
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installed size is 11.5Mb
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html_describe_con: multiple local function definitions for ‘g’ with
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘glmmADMB’
Package suggested but not available for checking: ‘microViz’
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installed size is  9.9Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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installed size is 15.9Mb
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'LazyData' is specified without a 'data' directory
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Note: skipping ‘Ch_cluster_analysis.Rnw’ due to unavailable dependencies:
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'LazyData' is specified without a 'data' directory
installed size is 69.9Mb
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GNU make is a SystemRequirements.
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installed size is  5.9Mb
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Package suggested but not available for checking: ‘HTSFilter’
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checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
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installed size is  8.0Mb
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Package suggested but not available for checking: ‘hurricaneexposuredata’
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installed size is 41.2Mb
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘microViz’
installed size is  8.0Mb
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installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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Package suggested but not available for checking: ‘flowCore’
installed size is 21.6Mb
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Error(s) in re-building vignettes:
--- re-building ‘hypergeometric.Rnw’ using Sweave
Loading required package: hypergeo
Loading required package: elliptic

Attaching package: ‘elliptic’

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

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Error: processing vignette 'hypergeometric.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'hypergeometric.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘hypergeometric.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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installed size is  5.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
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Specified C++11: please drop specification unless essential
installed size is  7.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SparkR’
installed size is  5.1Mb
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installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
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installed size is  6.4Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘LTRCtrees’
Package unavailable to check Rd xrefs: ‘LTRCtrees’
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Package suggested but not available for checking: ‘icd’
installed size is  5.8Mb
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checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
installed size is 15.6Mb
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Package suggested but not available for checking: ‘mixAK’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 32.2Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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Package suggested but not available for checking: ‘IFCdata’
installed size is  7.5Mb
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'LazyData' is specified without a 'data' directory
installed size is 24.9Mb
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 34.7Mb
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installed size is 23.5Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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Specified C++11: please drop specification unless essential
installed size is  5.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
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installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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installed size is 95.2Mb
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GNU make is a SystemRequirements.
installed size is 12.3Mb
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Specified C++11: please drop specification unless essential
installed size is  5.0Mb
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Specified C++11: please drop specification unless essential
installed size is  6.7Mb
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GNU make is a SystemRequirements.
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installed size is 12.5Mb
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Specified C++11: please drop specification unless essential
Package unavailable to check Rd xrefs: ‘minfi’
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'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘gurobi’
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Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
installed size is 10.6Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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installed size is 30.6Mb
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installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc   9.7Mb
Specified C++11: please drop specification unless essential
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Errors in running code in vignettes:
when running code in ‘PennsylvaniaWarbler.Rmd’
  ...
Loading required package: PointedSDMs
Loading required package: inlabru
Loading required package: fmesher
Loading required package: R6

> library(USAboundaries)

  When sourcing ‘PennsylvaniaWarbler.R’:
Error: there is no package called ‘USAboundaries’
Execution halted
when running code in ‘RedList.Rmd’
  ...
Loading required package: PointedSDMs
Loading required package: inlabru
Loading required package: fmesher
Loading required package: R6

> library(INLA)

  When sourcing ‘RedList.R’:
Error: there is no package called ‘INLA’
Execution halted
when running code in ‘Richness.Rmd’
  ...
Loading required package: PointedSDMs
Loading required package: inlabru
Loading required package: fmesher
Loading required package: R6

> library(INLA)

  When sourcing ‘Richness.R’:
Error: there is no package called ‘INLA’
Execution halted

  ‘PennsylvaniaWarbler.Rmd’ using ‘UTF-8’... failed
  ‘RedList.Rmd’ using ‘UTF-8’... failed
  ‘Richness.Rmd’ using ‘UTF-8’... failed
Specified C++11: please drop specification unless essential
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘surveyspec’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data           1.4Mb
    libs           1.9Mb
    shiny-server   1.0Mb
Specified C++11: please drop specification unless essential
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rhdf5’
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Package suggested but not available for checking: ‘Rmpi’
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xcms’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   3.3Mb
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
installed size is 95.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
    libs  89.9Mb
GNU make is a SystemRequirements.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  16.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘iucnrdata’
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          17.3Mb
GNU make is a SystemRequirements.
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  31.1Mb
Packages suggested but not available for checking: 'lfa', 'gcatest'
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   4.0Mb
    help      2.0Mb
installed size is 103.7Mb
  sub-directories of 1Mb or more:
    libs  102.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Specified C++11: please drop specification unless essential
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.4Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    i18n   6.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.9Mb
Package suggested but not available for checking: ‘remMap’
'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   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    examples      2.8Mb
    htmlwidgets   1.1Mb
    www           2.7Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kanjistat.data’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   8.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    help   2.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RGeostats’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pwalign’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kadmin’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.1Mb
'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:
    R      2.0Mb
    doc    1.7Mb
    help   1.1Mb
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘mixAK’
Package unavailable to check Rd xrefs: ‘mixAK’
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'xcms', 'MSnbase'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘VariantAnnotation’
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 59.1Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  54.7Mb
GNU make is a SystemRequirements.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 46.2Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  43.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    doc       1.5Mb
    extdata   1.1Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   9.6Mb
installed size is 95.4Mb
  sub-directories of 1Mb or more:
    libs  94.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    libs  44.1Mb
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      8.2Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
installed size is 71.9Mb
  sub-directories of 1Mb or more:
    libs  71.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘org.Mm.eg.db’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 22-30 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs      22.3Mb
    testdata   1.3Mb
Package suggested but not available for checking: ‘pbkrtest’
Package unavailable to check Rd xrefs: ‘pbkrtest’
installed size is 55.3Mb
  sub-directories of 1Mb or more:
    libs  54.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
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    R              2.0Mb
    doc-overview   2.2Mb
installed size is  6.3Mb
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    libs   5.9Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
Packages suggested but not available for checking: 'car', 'dynlm', 'AER'
Package unavailable to check Rd xrefs: ‘car’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘graph’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   5.3Mb
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Specified C++11: please drop specification unless essential
installed size is 64.4Mb
  sub-directories of 1Mb or more:
    libs  63.9Mb
'LazyData' is specified without a 'data' directory
installed size is 35.0Mb
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    doc    1.7Mb
    libs  33.0Mb
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

SUMMARY: processing the following file failed:
  ‘localsolver.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
installed size is 25.1Mb
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Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’
Specified C++11: please drop specification unless essential
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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installed size is  6.5Mb
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Package required but not available: ‘QSutils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Malformed Description field: should contain one or more complete sentences.
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Error: package or namespace load failed for ‘LSTbook’:
 .onLoad failed in loadNamespace() for 'LSTbook', details:
  call: loadNamespace(name)
  error: there is no package called ‘ggformula’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
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installed size is  6.0Mb
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installed size is 32.8Mb
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GNU make is a SystemRequirements.
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installed size is  6.9Mb
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Package suggested but not available for checking: ‘dittoSeq’
Packages suggested but not available for checking:
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Problems with news in ‘NEWS.md’:
No news entries found.
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Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 11.0Mb
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installed size is  5.1Mb
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installed size is 10.2Mb
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
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installed size is  5.5Mb
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installed size is 12.5Mb
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GNU make is a SystemRequirements.
installed size is  5.4Mb
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installed size is  5.8Mb
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GNU make is a SystemRequirements.
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
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checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
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installed size is 10.2Mb
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GNU make is a SystemRequirements.
installed size is  5.7Mb
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installed size is  8.7Mb
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installed size is 13.3Mb
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installed size is  8.2Mb
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GNU make is a SystemRequirements.
qr.X: no visible binding for global variable ‘R’
Undefined global functions or variables:
  R
'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  6.1Mb
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'LazyData' is specified without a 'data' directory
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installed size is 16.4Mb
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Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

> fitBernoulli <- mcemGLMM(fixed = Mate ~ 0 + Cross, 
+     random = list(~0 + Female, ~0 + Male), data = salamander, 
+     family = "bernoulli", vcD .... [TRUNCATED] 

Execution halted

... incomplete output.  Crash?

  ‘mcemGLM-vignette.Rnw’... failed to complete the test
* checking re-building of vignette outputs ...* using check arguments '--no-clean-on-error '
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
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checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
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installed size is 38.8Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 16.3Mb
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'LazyData' is specified without a 'data' directory
installed size is 18.6Mb
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Specified C++11: please drop specification unless essential
installed size is  7.4Mb
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Package suggested but not available for checking: ‘cmdstanr’
installed size is  6.5Mb
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checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
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checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
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installed size is  7.6Mb
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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Package suggested but not available for checking: ‘cmdstanr’
installed size is 64.7Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.9Mb
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'LazyData' is specified without a 'data' directory
installed size is 19.5Mb
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ADPopSel: no visible global function definition for ‘%dorng%’
ADRand: no visible global function definition for ‘%dorng%’
ADSSMod: no visible global function definition for ‘%dorng%’
ADTreatSel: no visible global function definition for ‘%dorng%’
ClustRand: no visible global function definition for ‘%dorng%’
EventPred: no visible global function definition for ‘%dorng%’
FutRuleNCores: no visible global function definition for ‘%dorng%’
MultAdj1NCores: no visible global function definition for ‘%dorng%’
MultAdj2NCores: no visible global function definition for ‘%dorng%’
MultAdj3NCores: no visible global function definition for ‘%dorng%’
Undefined global functions or variables:
  %dorng%
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 157.0Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
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Package suggested but not available for checking: ‘INLA’
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installed size is 109.1Mb
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GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'ropls', 'xcms'
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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installed size is  5.2Mb
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installed size is 14.4Mb
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Packages suggested but not available for checking:
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Package suggested but not available for checking: ‘caret’
installed size is  5.2Mb
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installed size is 20.2Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘InteractiveComplexHeatmap’
installed size is 56.8Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
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Package suggested but not available for checking: ‘INLA’
installed size is 13.3Mb
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installed size is 28.5Mb
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'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
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'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 19.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
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Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'
installed size is  7.4Mb
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Specified C++11: please drop specification unless essential
installed size is  9.4Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dada2’
Package required but not available: ‘microbiome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19',
  'BSgenome.Mmusculus.UCSC.mm10'
Running examples in ‘MicroSEC-Ex.R’ failed
The error most likely occurred in:

> ### Name: fun_load_genome
> ### Title: Genome loading function.
> ### Aliases: fun_load_genome
> 
> ### ** Examples
> 
> fun_load_genome("Human")
Error: Install BSgenome.Hsapiens.UCSC.hg38 package.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using rmarkdown

Quitting from lines 125-195 [analysis] (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'BSgenome.Hsapiens.UCSC.hg38'
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Execution halted
installed size is 20.5Mb
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    lib    9.0Mb
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installed size is  5.5Mb
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    doc    1.7Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘midfielddata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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Package suggested but not available for checking: ‘gurobi’
installed size is 15.4Mb
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    libs  14.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    data   5.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
Package required but not available: ‘InteractiveComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 22.8Mb
  sub-directories of 1Mb or more:
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installed size is 43.5Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 44.3Mb
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    redengine  42.7Mb
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installed size is 112.9Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  9.3Mb
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Packages unavailable to check Rd xrefs: ‘lme4’, ‘mixAK’
Package required but not available: ‘dada2’

Packages suggested but not available for checking: 'ANCOMBC', 'mia'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
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installed size is  6.8Mb
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Package suggested but not available for checking: ‘glmmTMB’
Packages suggested but not available for checking:
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installed size is 25.2Mb
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installed size is  7.1Mb
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Specified C++11: please drop specification unless essential
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Package which this enhances but not available for checking: ‘pbdMPI’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
installed size is 41.8Mb
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checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
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checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘mixRasch’
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installed size is 12.1Mb
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installed size is  8.3Mb
  sub-directories of 1Mb or more:
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    libs   4.5Mb
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: ‘genefilter’
installed size is  5.2Mb
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    help   2.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'minfi', 'IlluminaHumanMethylation450kmanifest'
Packages suggested but not available for checking:
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  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 244.5Mb
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Package suggested but not available for checking: ‘mlr3proba’
Package unavailable to check Rd xrefs: ‘mlr3proba’
Package suggested but not available for checking: ‘Rmpi’
installed size is  5.6Mb
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    data   2.3Mb
installed size is  6.2Mb
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    libs   5.9Mb
'LazyData' is specified without a 'data' directory
installed size is 141.3Mb
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    libs  139.3Mb
GNU make is a SystemRequirements.
installed size is 48.9Mb
  sub-directories of 1Mb or more:
    libs  48.4Mb
installed size is 30.0Mb
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    libs  29.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
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    images   1.1Mb
    shiny   14.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  14.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 19.0Mb
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    libs  18.9Mb
'LazyData' is specified without a 'data' directory
installed size is 121.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'doMPI', 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Package required but not available: ‘doMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR'
'LazyData' is specified without a 'data' directory
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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    data   5.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘survey’
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installed size is  6.1Mb
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    libs   4.4Mb
installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
installed size is 10.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
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    doc    1.7Mb
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installed size is  7.3Mb
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installed size is 14.8Mb
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Packages suggested but not available for checking: 'fftw', 'RODBC'
Packages unavailable to check Rd xrefs: ‘seewave’, ‘RODBC’
Package suggested but not available for checking: ‘lixoftConnectors’
installed size is  5.9Mb
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GNU make is a SystemRequirements.
installed size is 11.0Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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    raster   2.2Mb
Package suggested but not available for checking: ‘ergm’
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installed size is  5.4Mb
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Error: there is no package called ‘knitr’
Call sequence:
14: doWithOneRestart(return(expr), restart)
13: withOneRestart(expr, restarts[[1L]])
12: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
11: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
10: asNamespace(ns)
9: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
7: asNamespace(ns)
6: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPat
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘knitr’
Calls: <Anonymous>
Execution halted
Error: package or namespace load failed for ‘movieROC’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘knitr’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, cha
Execution halted
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  5.4Mb
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    libs   4.8Mb
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
Packages suggested but not available for checking: 'mvoutlier', 'glmulti'
Package suggested but not available for checking: ‘rhdf5’
installed size is  9.7Mb
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    libs   8.5Mb
'LazyData' is specified without a 'data' directory
installed size is 94.2Mb
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    libs  93.8Mb
GNU make is a SystemRequirements.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  12.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   4.5Mb
    libs   3.6Mb
installed size is 45.8Mb
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    libs  45.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R   6.0Mb
Package suggested but not available for checking: ‘ICAMS’
'LazyData' is specified without a 'data' directory
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 10.0Mb
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    doc    1.5Mb
    libs   7.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'switchBox', 'leukemiasEset'
Package suggested but not available for checking: ‘cmdstanr’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is 12.5Mb
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    libs  11.6Mb
'LazyData' is specified without a 'data' directory
installed size is 97.5Mb
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Package suggested but not available for checking: ‘statnet’
installed size is 278.5Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.2Mb
    libs  271.5Mb
GNU make is a SystemRequirements.
installed size is  6.1Mb
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Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
installed size is 36.5Mb
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    libs  36.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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    doc    2.6Mb
    help   2.2Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Package suggested but not available for checking: ‘cmdstanr’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    2.0Mb
    libs   1.8Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
Package unavailable to check Rd xrefs: ‘sampleSelection’
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
Packages suggested but not available for checking: 'BioNet', 'DLBCL'
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
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installed size is  6.0Mb
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    data   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Package which this enhances but not available for checking: ‘asreml’
installed size is 16.3Mb
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    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    data     2.9Mb
    libs    24.0Mb
    models   1.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Specified C++11: please drop specification unless essential
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
Error(s) in re-building vignettes:
  ...
--- re-building ‘NBLAST-Clustering.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 21:31:32.757 R[43986:2287591920] XType: Using static font registry.

Quitting from lines 57-60 [unnamed-chunk-5] (NBLAST-Clustering.Rmd)
Error: processing vignette 'NBLAST-Clustering.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. See here to learn more https://bookdown.org/yihui/rmarkdown-cookbook/install-pandoc.html
--- failed re-building ‘NBLAST-Clustering.Rmd’

SUMMARY: processing the following file failed:
  ‘NBLAST-Clustering.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
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    doc    1.7Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.5Mb
    libs   4.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rhdf5’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Specified C++11: please drop specification unless essential
installed size is 12.8Mb
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    libs  12.5Mb
Specified C++11: please drop specification unless essential
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.6Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  17.5Mb
Package suggested but not available for checking: ‘fastshp’
installed size is  6.8Mb
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    doc    1.6Mb
    libs   4.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.6Mb
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 233.3Mb
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    libs  232.5Mb
GNU make is a SystemRequirements.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Specified C++14: please drop specification unless essential
'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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    4.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
installed size is  5.2Mb
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    doc   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is 44.1Mb
  sub-directories of 1Mb or more:
    CppCode        3.9Mb
    R              8.1Mb
    classic-bugs   1.5Mb
    include       11.5Mb
    libs          18.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
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Specified C++11: please drop specification unless essential
installed size is 20.5Mb
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    R      1.0Mb
    libs  18.9Mb
installed size is  6.1Mb
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    extdata   3.7Mb
Package suggested but not available for checking: ‘csampling’
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
Package unavailable to check Rd xrefs: ‘csampling’
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Package suggested but not available for checking: ‘INLA’
installed size is  5.7Mb
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Package suggested but not available for checking: ‘doMPI’
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Package suggested but not available for checking: ‘simpar’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
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    libs   5.2Mb
    mods   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    libs       3.2Mb
    tinytest   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
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checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 13.7Mb
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installed size is  6.3Mb
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installed size is 11.1Mb
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'LazyData' is specified without a 'data' directory
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installed size is 100.3Mb
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'LazyData' is specified without a 'data' directory
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installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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Package suggested but not available for checking: ‘cmdstanr’
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
Package required but not available: ‘TCGAbiolinks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
installed size is 277.5Mb
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘openNLPmodels.en’
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installed size is  9.3Mb
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installed size is 11.6Mb
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installed size is 34.9Mb
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Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
installed size is  7.9Mb
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'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘rrelaxiv’
Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  6.6Mb
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installed size is 10.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
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installed size is  5.3Mb
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Package suggested but not available for checking: ‘Rcplex’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
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checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
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'LazyData' is specified without a 'data' directory
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Packages suggested but not available for checking:
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installed size is  6.8Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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Package suggested but not available for checking: ‘CorShrink’
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installed size is  5.2Mb
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checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
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Package suggested but not available for checking: ‘ggeffects’
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Specified C++11: please drop specification unless essential
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installed size is  7.1Mb
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'LazyData' is specified without a 'data' directory
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installed size is 84.5Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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Error(s) in re-building vignettes:
--- re-building ‘partitionspaper.Rnw’ using Sweave
Loading required package: partitions
Error: processing vignette 'partitionspaper.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'partitionspaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘partitionspaper.Rnw’

--- re-building ‘scrabble.Rnw’ using Sweave
Error: processing vignette 'scrabble.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'scrabble.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘scrabble.Rnw’

--- re-building ‘setpartitions.Rnw’ using Sweave
Loading required package: partitions
Error: processing vignette 'setpartitions.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'setpartitions.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘setpartitions.Rnw’

SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
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Package required but not available: ‘ggkegg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘anomalize’
installed size is  5.6Mb
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Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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installed size is  7.7Mb
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installed size is  5.4Mb
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installed size is  6.6Mb
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installed size is  7.5Mb
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installed size is  7.6Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/pbdMPI.Rcheck/00install.out’ for details.
Package required but not available: ‘pbdMPI’

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
Package suggested but not available for checking: ‘PerformanceAnalytics’
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installed size is  5.4Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 28.2Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
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installed size is 140.0Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 33.3Mb
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Specified C++11: please drop specification unless essential
installed size is 32.7Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtreeExtra’
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘PythonInR’
installed size is 21.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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Packages suggested but not available for checking:
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Packages unavailable to check Rd xrefs: ‘fields’, ‘gstat’, ‘car’
installed size is 126.0Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
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checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
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installed size is  6.0Mb
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installed size is 10.2Mb
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installed size is 51.5Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
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checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
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installed size is 11.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lme4’
Package unavailable to check Rd xrefs: ‘lme4’
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checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
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checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.1Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: ‘phase1RMD’
Package suggested but not available for checking: ‘BiocParallel’
Packages suggested but not available for checking:
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installed size is  5.4Mb
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installed size is  7.3Mb
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installed size is 49.0Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
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installed size is 86.7Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘phyloseq’
installed size is 63.8Mb
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installed size is  5.3Mb
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Packages suggested but not available for checking: 'INLA', 'DHARMa', 'rr2'
installed size is 12.4Mb
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checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
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checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
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installed size is 11.5Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘httk’
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Package suggested but not available for checking: ‘slingshot’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ellipse’
installed size is  6.7Mb
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installed size is  5.7Mb
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installed size is 18.8Mb
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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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
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Package suggested but not available for checking: ‘pmartRdata’
installed size is  7.7Mb
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Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MSnbase’
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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
Problems with news in ‘NEWS.md’:
No news entries found.
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Errors in running code in vignettes:
when running code in ‘Marked_Point_Process.Rmd’
  ...

> library(ggplot2)

> library(inlabru)

> library(INLA)

  When sourcing ‘Marked_Point_Process.R’:
Error: there is no package called ‘INLA’
Execution halted
when running code in ‘Setophaga.Rmd’
  ...

> args(datasetOut)
function (model, dataset, predictions = TRUE) 
NULL

> library(INLA)

  When sourcing ‘Setophaga.R’:
Error: there is no package called ‘INLA’
Execution halted
when running code in ‘Solitary_tinamou.Rmd’
  ...
terra 1.7.78

> library(ggpolypath)
Loading required package: ggplot2

> library(INLA)

  When sourcing ‘Solitary_tinamou.R’:
Error: there is no package called ‘INLA’
Execution halted
when running code in ‘Spatiotemporal_example.Rmd’
  ...

> library(ggplot2)

> library(spocc)

> library(INLA)

  When sourcing ‘Spatiotemporal_example.R’:
Error: there is no package called ‘INLA’
Execution halted

  ‘Marked_Point_Process.Rmd’ using ‘UTF-8’... failed
  ‘Setophaga.Rmd’ using ‘UTF-8’... failed
  ‘Solitary_tinamou.Rmd’ using ‘UTF-8’... failed
  ‘Spatiotemporal_example.Rmd’ using ‘UTF-8’... failed
'LazyData' is specified without a 'data' directory
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘pollimetrydata’
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installed size is  6.4Mb
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Package suggested but not available for checking: ‘VariantAnnotation’
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Package unavailable to check Rd xrefs: ‘VariantAnnotation’
installed size is 18.0Mb
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installed size is  7.0Mb
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GNU make is a SystemRequirements.
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installed size is  6.7Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
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installed size is 39.4Mb
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Package suggested but not available for checking: ‘lme4’
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Package suggested but not available for checking: ‘rstan’
Package unavailable to check Rd xrefs: ‘rstan’
Specified C++11: please drop specification unless essential
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checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
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checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
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Specified C++11: please drop specification unless essential
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
No news entries found.
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installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.5Mb
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Package suggested but not available for checking: ‘bipartite’
installed size is  7.4Mb
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Packages suggested but not available for checking:
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installed size is 10.7Mb
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Packages suggested but not available for checking:
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installed size is 19.8Mb
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Packages suggested but not available for checking: 'cmdstanr', 'iwmm'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
installed size is 20.7Mb
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'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
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Package required but not available: ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
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installed size is 34.4Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cin’
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Package suggested but not available for checking: ‘rdt’
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘cmdstanr’
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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installed size is  7.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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installed size is 11.5Mb
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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'LazyData' is specified without a 'data' directory
installed size is 27.6Mb
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iclust: no visible binding for global variable ‘use’
Undefined global functions or variables:
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'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
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installed size is 47.6Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is 15.5Mb
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'LazyData' is specified without a 'data' directory
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
installed size is  7.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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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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Package suggested but not available for checking: ‘spDataLarge’
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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'LazyData' is specified without a 'data' directory
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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.
installed size is  9.2Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Packages suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
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installed size is  7.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘survey’
Package unavailable to check Rd xrefs: ‘survey’
installed size is  8.9Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘fastshp’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘ReGenesees’
Warning: package needs dependence on R (>= 2.10)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘bootmlm’
'library' or 'require' call to ‘RDCOMClient’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
installed size is  7.9Mb
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'library' or 'require' calls in package code:
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  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: ‘BRugs’
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is 11.5Mb
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installed size is  7.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'batchelor', 'slingshot'
installed size is 10.8Mb
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'LazyData' is specified without a 'data' directory
installed size is 25.4Mb
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installed size is  5.7Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 46.0Mb
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installed size is  5.8Mb
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installed size is 35.7Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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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Packages suggested but not available for checking: 'xcms', 'MSnbase'
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Spectra’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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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
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  8.1Mb
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'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘RankAggreg.Rnw’ using Sweave
Loading required package: cluster
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: ‘kohonen’

The following object is masked from ‘package:mclust’:

    map

Error: processing vignette 'RankAggreg.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RankAggreg.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.28 \usepackage
                [mathcal]{euscript}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘RankAggreg.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
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    libs   4.6Mb
installed size is  6.5Mb
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    libs   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      9.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 68.5Mb
  sub-directories of 1Mb or more:
    libs  67.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
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    libs  12.2Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    doc       2.6Mb
    rstudio   1.6Mb
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is 10.6Mb
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    data   5.6Mb
    etc    1.9Mb
    po     1.2Mb
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs  10.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
'LazyData' is specified without a 'data' directory
installed size is 25.2Mb
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    libs  24.2Mb
Package suggested but not available for checking: ‘raybevel’
installed size is  7.2Mb
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    data   2.9Mb
    libs   3.3Mb
installed size is 13.4Mb
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    libs  12.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      3.8Mb
GNU make is a SystemRequirements.
installed size is 67.5Mb
  sub-directories of 1Mb or more:
    libs  65.6Mb
GNU make is a SystemRequirements.
installed size is 60.1Mb
  sub-directories of 1Mb or more:
    libs  59.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rhdf5’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rblpapi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 64.3Mb
  sub-directories of 1Mb or more:
    libs  63.6Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    cont  20.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.5Mb
    po    2.4Mb
Package suggested but not available for checking: ‘conics’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Packages suggested but not available for checking:
  'ROntoTools', 'hgu133plus2.db', 'pd.hg.u133.plus.2', 'oligo'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rcplex.Rcheck/00install.out’ for details.
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  18.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
    libs      2.2Mb
Specified C++11: please drop specification unless essential
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 40.3Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
    libs      2.3Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    include  46.0Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    include   9.5Mb
    libs     24.7Mb
Specified C++11: please drop specification unless essential
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcppMeCab.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Specified C++11: please drop specification unless essential
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      5.0Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    include        7.2Mb
    jsonexamples   3.8Mb
    libs          12.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      5.9Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      4.6Mb
    data   1.5Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'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.
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   3.0Mb
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    libs        1.4Mb
    redengine  42.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Package suggested but not available for checking: ‘Rmpi’
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs  14.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.8Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      4.8Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'cdparcoord', 'partools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggpubr’
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'PADOG', 'GSVA'
Packages unavailable to check Rd xrefs: ‘GSVA’, ‘PADOG’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   7.1Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.2Mb
    libs  13.7Mb
GNU make is a SystemRequirements.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Package suggested but not available for checking: ‘resourcecodedata’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
installed size is 28.5Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs     24.4Mb
    models    1.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Package suggested but not available for checking: ‘ccdata’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘btergm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.4Mb
installed size is 46.0Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Running ‘testthat.R’ [64s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. ├─testthat::expect_error(...) at test-forestry.R:48:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─Rforestry::forestry(x = iris[, -1], y = iris[, 1], seed = seed_i)
    7.   └─base::tryCatch(...)
    8.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.         └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1422 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    fonts   1.5Mb
    libs   25.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Running examples in ‘ridge-Ex.R’ failed
The error most likely occurred in:

> ### Name: pvals
> ### Title: Compute p-values for ridgeLinear and ridgeLogistic models
> ### Aliases: pvals pvals.ridgeLinear pvals.ridgeLogistic
> ###   plot.pvalsRidgeLinear plot.pvalsRidgeLogistic print.pvalsRidgeLinear
> ###   print.pvalsRidgeLogistic
> 
> ### ** Examples
> 
> data(GenBin)
> mod <- logisticRidge(Phenotypes ~ ., data = as.data.frame(GenBin))

Execution halted
Specified C++11: please drop specification unless essential
installed size is 18.4Mb
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    data   1.6Mb
    libs  16.0Mb
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘portfolioBacktest’
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  20.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.7Mb
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 55.9Mb
  sub-directories of 1Mb or more:
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    libs     51.7Mb
installed size is 12.1Mb
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installed size is 10.8Mb
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installed size is 10.3Mb
  sub-directories of 1Mb or more:
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installed size is 28.3Mb
  sub-directories of 1Mb or more:
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    exe  23.8Mb
'LazyData' is specified without a 'data' directory
installed size is 18.7Mb
  sub-directories of 1Mb or more:
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installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
installed size is  9.2Mb
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installed size is 20.1Mb
  sub-directories of 1Mb or more:
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    libs   17.0Mb
'LazyData' is specified without a 'data' directory
installed size is 165.9Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 72.0Mb
  sub-directories of 1Mb or more:
    include   7.1Mb
    lib      37.8Mb
    libs     26.6Mb
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'DoubletFinder', 'EnhancedVolcano', 'RcppPlanc', 'reactome.db'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rnaturalearthhires’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
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    libs   5.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RMark.Rcheck/00install.out’ for details.
Warning: Software mark not found in path.
         If you have mark executable, you will need to set MarkPath object to its location (e.g. MarkPath="C:/Users/Jeff Laake/Desktop"

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
installed size is 135.1Mb
  sub-directories of 1Mb or more:
    libs  134.7Mb
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RmecabKo.Rcheck/00install.out’ for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   6.0Mb
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
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installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       1.1Mb
    minizinc   3.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    libs  38.4Mb
installed size is 27.7Mb
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    libs  27.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rmpi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 85.0Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
GNU make is a SystemRequirements.
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.2Mb
Package required but not available: ‘R4RNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
Package suggested but not available for checking: ‘recount3’
installed size is  5.5Mb
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    doc    2.3Mb
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
Packages which this enhances but not available for checking:
  'pbdMPI', 'Rmpi'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Packages unavailable to check Rd xrefs: ‘pbdMPI’, ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 120.9Mb
  sub-directories of 1Mb or more:
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    libs     118.7Mb
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
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    libs  12.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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installed size is 11.3Mb
  sub-directories of 1Mb or more:
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installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
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installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error(s) in re-building vignettes:
--- re-building ‘RobPer_vignette.Rnw’ using Sweave
Loading required package: robustbase
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve

Loading required package: splines
Loading required package: BB
Loading required package: rgenoud
##  rgenoud (Version 5.9-0.3, Build Date: 2022-04-19)
##  See http://sekhon.berkeley.edu/rgenoud for additional documentation.
##  Please cite software as:
##   Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
##   ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
##   Journal of Statistical Software, 42(11): 1-26. 
##

Error: processing vignette 'RobPer_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {thumbpdf,lmodern}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'RobPer_vignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is 97.5Mb
  sub-directories of 1Mb or more:
    libs  96.7Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘ivgets’
Package unavailable to check Rd xrefs: ‘ivgets’
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
Specified C++11: please drop specification unless essential
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              5.1Mb
    simulationStudy   1.5Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'car', 'HH'
Package unavailable to check Rd xrefs: ‘HH’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         3.7Mb
    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
sh: cmake: command not found
------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

 - installr::install.cmake()  (Windows; inside the R console)
 - yum install cmake          (Fedora/CentOS; inside a terminal)
 - apt install cmake          (Debian/Ubuntu; inside a terminal)
 - brew install cmake         (MacOS; inside a terminal with Homebrew)
 - port install cmake         (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: <https://cmake.org/>

-------------------------------------------------------


It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/ROracle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MBESS’
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    libs   8.3Mb
Package suggested but not available for checking: ‘RandomFields’
installed size is 61.1Mb
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    libs  59.9Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
installed size is 53.1Mb
  sub-directories of 1Mb or more:
    libs  53.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 102.8Mb
  sub-directories of 1Mb or more:
    libs  102.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
Errors in running code in vignettes:
when running code in ‘Using.RRPP.Rmd’
  ...
> fit.par <- lm(fit$call$f1, data = fit$LM$data)

> all.equal(fit$LM$coefficients, fit.par$coefficients)
[1] TRUE

> summary(manova(fit.par))

  When sourcing ‘Using.RRPP.R’:
Error: residuals have rank 49 < 112
Execution halted

  ‘ANOVA.vs.MANOVA.Rmd’ using ‘UTF-8’... [28s/42s] OK
  ‘Using.RRPP.Rmd’ using ‘UTF-8’... failed
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fields', 'qgraph'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  24.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    help   1.5Mb
Specified C++11: please drop specification unless essential
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  47.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 299.3Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.7Mb
    libs  291.8Mb
GNU make is a SystemRequirements.
installed size is 96.4Mb
  sub-directories of 1Mb or more:
    libs  96.1Mb
GNU make is a SystemRequirements.
installed size is 58.5Mb
  sub-directories of 1Mb or more:
    libs  57.9Mb
GNU make is a SystemRequirements.
installed size is 49.8Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib   34.7Mb
    libs  11.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggpubr’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    external   1.6Mb
    libs       3.9Mb
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
Specified C++11: please drop specification unless essential
installed size is 28.0Mb
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    libs  27.6Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    swipl  27.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.8Mb
    help   2.4Mb
'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   5.0Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    rmarkdown  11.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Gviz’
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs       2.0Mb
    projects   2.9Mb
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 116.0Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    libs  114.2Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
Specified C++11: please drop specification unless essential
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  19.9Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 222.9Mb
  sub-directories of 1Mb or more:
    data    1.5Mb
    libs  220.5Mb
GNU make is a SystemRequirements.
Running examples in ‘RtsEva-Ex.R’ failed
The error most likely occurred in:

> ### Name: tsEstimateAverageSeasonality
> ### Title: Estimate Average Seasonality
> ### Aliases: tsEstimateAverageSeasonality
> 
> ### ** Examples
> 
> timeAndSeries <- ArdecheStMartin
> timeStamps <- ArdecheStMartin[,1]
> series  <- ArdecheStMartin[,2]
> timeWindow <- 30*365  # 30 years
> rs <- tsEvaDetrendTimeSeries(timeStamps, series, timeWindow)
> nRunMn <- rs@nRunMn
> cat("computing trend seasonality ...\n")
computing trend seasonality ...
> seasonalitySeries <- rs@detrendSeries
> result <- tsEstimateAverageSeasonality(timeStamps, seasonalitySeries, timeWindow=rs@nRunMn)
Warning in pracma::interp1(avgTmStamp, monthAvgVec, timeStampsN, method = "spline") :
  Points in argument in 'x' unsorted; will be sorted.
Warning in pracma::interp1(avgTmStamp, monthAvgVex, timeStampsN, method = "spline") :
  Points in argument in 'x' unsorted; will be sorted.
> plot(result$regime, type = "l", xlab = "Day", ylab = "Regime", main = "Estimated Regime")
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot -> plot.default -> localWindow -> plot.window
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  6.2Mb
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    extdata   1.0Mb
    libs      4.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
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    libs   2.5Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
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    libs   6.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
'library' or 'require' calls in package code:
  ‘nimble’ ‘nimbleAPT’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmmADMB’
Package required but not available: ‘GSVAdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 48.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gpuR’
installed size is  5.2Mb
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installed size is 59.2Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
installed size is  5.9Mb
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    extdata   2.4Mb
Specified C++11: please drop specification unless essential
installed size is 10.8Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘partykit’
Package unavailable to check Rd xrefs: ‘partykit’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.2Mb
  sub-directories of 1Mb or more:
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installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
  sub-directories of 1Mb or more:
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installed size is 11.2Mb
  sub-directories of 1Mb or more:
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installed size is  9.0Mb
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Specified C++11: please drop specification unless essential
installed size is  9.5Mb
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Specified C++14: please drop specification unless essential
installed size is 10.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.8Mb
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installed size is 12.3Mb
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Specified C++14: please drop specification unless essential
installed size is 38.0Mb
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checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.7Mb
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'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
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    libs  15.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lme4’
Note: skipping ‘my-vignette.Rnw’ due to unavailable dependencies: 'lme4'
installed size is 14.4Mb
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Specified C++11: please drop specification unless essential
installed size is 20.5Mb
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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 54.3Mb
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Specified C++11: please drop specification unless essential
installed size is 10.0Mb
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Packages suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
installed size is 47.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  6.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  5.3Mb
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Specified C++11: please drop specification unless essential
installed size is  5.2Mb
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GNU make is a SystemRequirements.
installed size is  6.3Mb
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installed size is  7.2Mb
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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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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installed size is  5.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Packages suggested but not available for checking:
  'dittoSeq', 'DropletUtils', 'Nebulosa'
Packages unavailable to check Rd xrefs: ‘DropletUtils’, ‘Nebulosa’
Package required but not available: ‘glmGamPoi’

Package suggested but not available for checking: ‘Linnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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    libs   2.9Mb
Packages suggested but not available for checking:
  'ontoProc', 'rrvgo', 'SingleCellSignalR'
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Package required and available but unsuitable version: ‘UCell’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘batchelor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘simplifyEnrichment’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/scorematchingad.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'AUCell', 'decoupleR', 'infercnv', 'Nebulosa'
Package unavailable to check Rd xrefs: ‘infercnv’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmGamPoi’
installed size is 21.2Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘oligoClasses’
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
Error(s) in re-building vignettes:
--- re-building ‘intro.Rnw’ using Sweave
scuba 1.11-1 
Type ‘help(scuba)’ for an introduction 
Read the warnings in ‘help(scuba.disclaimer)’ 
For news about changes to the package, type ‘news(package='scuba')’
scuba 1.11-1 
Type ‘help(scuba)’ for an introduction 
Read the warnings in ‘help(scuba.disclaimer)’ 
For news about changes to the package, type ‘news(package='scuba')’

Attaching package: ‘scuba’

The following objects are masked _by_ ‘.GlobalEnv’:

    pedro902, pedro903, pedro904, pedro922, pedro943, pedro944,
    pedro945, pedro946, pedro948, pedro949, pedro950

Error: processing vignette 'intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `anysize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \marginsize
               {2cm}{2cm}{2cm}{2cm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
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    libs   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sdcSpatial.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 190-192 (sdcSpatial.Rmd) 
Error: processing vignette 'sdcSpatial.Rmd' failed with diagnostics:
different crs
--- failed re-building ‘sdcSpatial.Rmd’

SUMMARY: processing the following file failed:
  ‘sdcSpatial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 89.3Mb
  sub-directories of 1Mb or more:
    libs  87.4Mb
Error(s) in re-building vignettes:
--- re-building ‘sdmvspecies.Rnw’ using Sweave
Loading required package: sp
[1] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio1.bil" 
[2] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio11.bil"
[3] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio12.bil"
[4] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio14.bil"
[5] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio16.bil"
[6] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio5.bil" 
[7] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio7.bil" 
Error: processing vignette 'sdmvspecies.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sdmvspecies.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sdmvspecies.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘sealasso.Rnw’ using Sweave
Loading required package: lars
Loaded lars 1.3

Error: processing vignette 'sealasso.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sealasso.tex' failed.
LaTeX errors:
! LaTeX Error: File `anysize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \marginsize
               {2.5cm}{2.5cm}{2.5cm}{2.5cm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sealasso.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'MuSiC', 'seAMLessData'
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R   8.6Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  15.4Mb
GNU make is a SystemRequirements.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.6Mb
'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:
    data   3.9Mb
    libs   7.8Mb
Packages required but not available: 'ggmsa', 'msa'

Package suggested but not available for checking: ‘org.Rn.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rsbml’
Packages suggested but not available for checking:
  'ArrayExpress', 'org.Mm.eg.db'
Package unavailable to check Rd xrefs: ‘ArrayExpress’
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
'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
Package suggested but not available for checking: ‘Rmpfr’
Package suggested but not available for checking: ‘Ecdat’
'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
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'blavaan', 'emmeans'
Package unavailable to check Rd xrefs: ‘blavaan’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   2.5Mb
Specified C++11: please drop specification unless essential
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs    21.1Mb
    models   1.6Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.0Mb
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.5Mb
Specified C++14: please drop specification unless essential
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Package suggested but not available for checking: ‘airway’
Packages suggested but not available for checking:
  'FactoMineR', 'descriptio'
installed size is 17.7Mb
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    doc    6.4Mb
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pwalign’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  54.5Mb
GNU make is a SystemRequirements.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
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
Packages suggested but not available for checking: 'HDF5Array', 'BPCells'
Packages suggested but not available for checking:
  'arrow', 'BPCells', 'monocle', 'presto'
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggraph’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 272.6Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    libs    266.1Mb
    sqlite    1.5Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: ‘tripack’
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    shinymgr    1.4Mb
    tutorials   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
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    www  10.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘edgeR’
Note: skipping ‘SIBER.Rnw’ due to unavailable dependencies: 'edgeR'
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installed size is  5.9Mb
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Packages suggested but not available for checking:
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installed size is  5.1Mb
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Packages unavailable to check Rd xrefs: ‘motifmatchr’, ‘TFBSTools’, ‘chromVAR’
Package suggested but not available for checking: ‘rhdf5’
Package required but not available: ‘GSVA’

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
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
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installed size is  7.3Mb
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installed size is  6.1Mb
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GNU make is a SystemRequirements.
installed size is 14.5Mb
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    libs  12.4Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  5.7Mb
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Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
Packages suggested but not available for checking:
  'quantreg', 'semTools', 'OpenMx', 'copula'
Package unavailable to check Rd xrefs: ‘copula’
Package suggested but not available for checking: ‘INLA’
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
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installed size is 22.7Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
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installed size is 13.1Mb
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Package which this enhances but not available for checking: ‘kmndirs’
installed size is  7.1Mb
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GNU make is a SystemRequirements.
installed size is 39.2Mb
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installed size is 33.1Mb
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installed size is  5.1Mb
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installed size is  5.9Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
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checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘gurobi’
installed size is  5.8Mb
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GNU make is a SystemRequirements.
installed size is  5.3Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
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Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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Package suggested but not available for checking: ‘demography’
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Problems with news in ‘NEWS.md’:
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
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Package required but not available: ‘GWASTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
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installed size is  5.7Mb
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Package suggested but not available for checking: ‘NLMR’
installed size is  6.8Mb
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Package suggested but not available for checking: ‘NLMR’
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installed size is  5.1Mb
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    R      2.1Mb
    java   1.8Mb
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Specified C++11: please drop specification unless essential
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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installed size is 15.1Mb
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S3 methods shown with full name in documentation object 'SparseM.ontology':
  ‘as.matrix.csr’ ‘is.matrix.csr’ ‘is.matrix.csc’ ‘is.matrix.ssr’
  ‘is.matrix.ssc’ ‘is.matrix.coo’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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installed size is 35.1Mb
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Package suggested but not available for checking: ‘INLA’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/spaths.Rcheck/00install.out’ for details.
Package required but not available: ‘SpatialExperiment’

Package suggested but not available for checking: ‘HDF5Array’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
installed size is 95.0Mb
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    help   1.7Mb
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Specified C++14: please drop specification unless essential
installed size is 14.1Mb
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    libs  12.5Mb
GNU make is a SystemRequirements.
installed size is  6.1Mb
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    libs   4.2Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
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    help   2.2Mb
installed size is  5.5Mb
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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  5.2Mb
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installed size is 13.4Mb
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    data   3.3Mb
    libs   9.5Mb
installed size is  6.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
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Package suggested but not available for checking: ‘spDataLarge’
installed size is  8.4Mb
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installed size is  5.9Mb
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installed size is  9.7Mb
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    etc   2.1Mb
Package suggested but not available for checking: ‘scRNAseq’
Running examples in ‘speaq-Ex.R’ failed
The error most likely occurred in:

> ### Name: BWR
> ### Title: BW ratio calculation
> ### Aliases: BWR
> 
> ### ** Examples
> 
> res=makeSimulatedData();
> X=res$data;
> groupLabel=res$label;
> peakList <- detectSpecPeaks(X,
+                             nDivRange = c(128),
+                             scales = seq(1, 16, 2),
+                             baselineThresh = 50000,
+                             SNR.Th = -1,
+                             verbose=FALSE
+ );
> resFindRef<- findRef(peakList);
> refInd <- resFindRef$refInd;
> maxShift = 50;
> Y <- dohCluster(X,
+                 peakList = peakList,
+                 refInd = refInd,
+                 maxShift  = maxShift,
+                 acceptLostPeak = TRUE, verbose=FALSE);
Warning in min(peakList) :
  no non-missing arguments to min; returning Inf
Warning in max(peakList) :
  no non-missing arguments to max; returning -Inf
Error in startP:(minpeakList - 1) : result would be too long a vector
Calls: dohCluster -> .withMaxShift -> hClustAlign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘classic_speaq_vignette.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 23:48:34.091 R[19637:2290508776] XType: Using static font registry.

Quitting from lines 111-120 [Spectral_alignment] (classic_speaq_vignette.Rmd)
Error: processing vignette 'classic_speaq_vignette.Rmd' failed with diagnostics:
result would be too long a vector
--- failed re-building ‘classic_speaq_vignette.Rmd’

--- re-building ‘speaq2_illustrations.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 23:48:40.223 R[20964:2290511430] XType: Using static font registry.

Quitting from lines 71-83 [detect winepeaks] (speaq2_illustrations.Rmd)
Error: processing vignette 'speaq2_illustrations.Rmd' failed with diagnostics:
invalid 'times' argument
--- failed re-building ‘speaq2_illustrations.Rmd’

SUMMARY: processing the following files failed:
  ‘classic_speaq_vignette.Rmd’ ‘speaq2_illustrations.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
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installed size is  6.0Mb
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Undocumented S4 methods:
  generic '[' and siglist 'SpectraInTime,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTime,missing,ANY,ANY'
  generic '[' and siglist 'SpectraInTime,missing,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,ANY,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,missing,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
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Specified C++11: please drop specification unless essential
installed size is  6.8Mb
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'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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'LazyData' is specified without a 'data' directory
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installed size is  6.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    libs   5.1Mb
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
installed size is  5.9Mb
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    R      2.0Mb
    data   1.8Mb
    doc    1.5Mb
Specified C++11: please drop specification unless essential
installed size is  6.6Mb
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    R      2.0Mb
    libs   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggraph’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
installed size is  7.1Mb
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installed size is 50.2Mb
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running examples in ‘spsurv-Ex.R’ failed
The error most likely occurred in:

> ### Name: bppo
> ### Title: Bernstein Polynomial Based Proportional Odds Model
> ### Aliases: bppo
> 
> ### ** Examples
> 
> 
> library("spsurv")
> data("veteran")
Warning in data("veteran") : data set ‘veteran’ not found
> 
> fit <- bppo(Surv(time, status) ~ karno + celltype,
+ data = veteran)
Error in optimHess(theta, fn, gr, control = list(fnscale = -1)) : 
  non-finite value supplied by optim
Calls: bppo ... spbp.mle -> <Anonymous> -> <Anonymous> -> .local -> optimHess
Execution halted
Running ‘testthat.R’ [17s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test.R:33:1'): (code run outside of `test_that()`) ──────────────────
  Error in `optimHess(theta, fn, gr, control = list(fnscale = -1))`: non-finite value supplied by optim
  Backtrace:
      ▆
   1. └─spsurv::bppo(Surv(time, status) ~ karno + factor(celltype), data = veteran) at test.R:33:0
   2.   └─spsurv:::spbp.default(...)
   3.     └─spsurv:::spbp.mle(standata = standata, ...)
   4.       ├─rstan::optimizing(...)
   5.       └─rstan::optimizing(...)
   6.         └─rstan (local) .local(object, ...)
   7.           └─stats::optimHess(theta, fn, gr, control = list(fnscale = -1))
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘ecpc’
installed size is  5.6Mb
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Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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GNU make is a SystemRequirements.
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Loading required package: mvtnorm
Error: processing vignette 'SSsimple.Snw' failed with diagnostics:
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LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SSsimple.Snw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
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Package suggested but not available for checking: ‘networksis’
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Loading required package: gnm
Loading required package: forecast
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LaTeX errors:
! LaTeX Error: File `ctable.sty' not found.

Type X to quit or <RETURN> to proceed,
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! Emergency stop.
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l.7 \usepackage
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!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'StMoMoVignette.Rnw'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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installed size is  9.8Mb
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Malformed Title field: should not end in a period.
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installed size is  9.3Mb
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installed size is 10.5Mb
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Package unavailable to check Rd xrefs: ‘HDoutliers’
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efpFunctional: multiple local function definitions for ‘plotProcess’
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mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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GNU make is a SystemRequirements.
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checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: ‘microbiome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Malformed Description field: should contain one or more complete sentences.
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GNU make is a SystemRequirements.
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Package which this enhances but not available for checking: ‘R2wd’
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/terra.Rcheck/00install.out’ for details.
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Problems with news in ‘NEWS.md’:
No news entries found.
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checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
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    Initial Release (v0.1.0)
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    Minor changes:
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Error(s) in re-building vignettes:
--- re-building ‘TQ00-introduction-to-tidyquant.Rmd’ using rmarkdown
--- finished re-building ‘TQ00-introduction-to-tidyquant.Rmd’

--- re-building ‘TQ01-core-functions-in-tidyquant.Rmd’ using rmarkdown
--- finished re-building ‘TQ01-core-functions-in-tidyquant.Rmd’

--- re-building ‘TQ02-quant-integrations-in-tidyquant.Rmd’ using rmarkdown
--- finished re-building ‘TQ02-quant-integrations-in-tidyquant.Rmd’

--- re-building ‘TQ03-scaling-and-modeling-with-tidyquant.Rmd’ using rmarkdown
Error: processing vignette 'TQ03-scaling-and-modeling-with-tidyquant.Rmd' failed with diagnostics:
Error writing to connection:  No space left on device
--- failed re-building ‘TQ03-scaling-and-modeling-with-tidyquant.Rmd’

--- re-building ‘TQ04-charting-with-tidyquant.Rmd’ using rmarkdown
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error: processing vignette 'TQ04-charting-with-tidyquant.Rmd' failed with diagnostics:
Error writing to connection:  No space left on device
--- failed re-building ‘TQ04-charting-with-tidyquant.Rmd’

--- re-building ‘TQ05-performance-analysis-with-tidyquant.Rmd’ using rmarkdown
--- finished re-building ‘TQ05-performance-analysis-with-tidyquant.Rmd’

--- re-building ‘TQ06-excel-in-r.Rmd’ using rmarkdown
--- finished re-building ‘TQ06-excel-in-r.Rmd’

SUMMARY: processing the following files failed:
  ‘TQ03-scaling-and-modeling-with-tidyquant.Rmd’
  ‘TQ04-charting-with-tidyquant.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘SingleR’
installed size is 47.1Mb
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Running ‘testthat.R’ [13s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidystats)
  This version of tidystats uses a new and improved way of structuring statistics. This breaks previous (major) versions of tidystats.
  > 
  > test_check("tidystats")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_glm.R:118:3'): glm anova works ───────────────────────────────
  `tidy_model` not equal to `expected_tidy_model`.
  Component "groups": Component 1: Component 2: Component 2: Component 2: Length mismatch: comparison on first 4 components
  Component "groups": Component 1: Component 2: Component 3: Component 2: Length mismatch: comparison on first 4 components
  Backtrace:
      ▆
   1. └─tidystats:::expect_equal_models(model = model, expected_tidy_model = expected_statistics$anova_glm) at test_glm.R:118:3
   2.   └─testthat::expect_equal(tidy_model, expected_tidy_model, tolerance = tolerance)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘rrelaxiv’
installed size is 58.4Mb
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checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'org.Rn.eg.db', 'org.Mm.eg.db'
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installed size is 98.9Mb
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GNU make is a SystemRequirements.
installed size is  5.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
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Specified C++14: please drop specification unless essential
installed size is  9.9Mb
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installed size is 30.3Mb
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GNU make is a SystemRequirements.
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installed size is  6.2Mb
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Package suggested but not available for checking: ‘stm’
Package unavailable to check Rd xrefs: ‘stm’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: ‘gurobi’
installed size is  7.4Mb
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installed size is 200.1Mb
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Package suggested but not available for checking: ‘toscaData’
installed size is  5.1Mb
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Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 13.0Mb
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    data  13.0Mb
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Package suggested but not available for checking: ‘competitiontoolbox’
Package unavailable to check Rd xrefs: ‘competitiontoolbox’
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘fwelnet’
installed size is  5.1Mb
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Package suggested but not available for checking: ‘Capr’
Packages required but not available: 'csaw', 'HiCDOC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘TreeDistData’
Package suggested but not available for checking: ‘Seurat’
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installed size is 10.4Mb
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installed size is  8.4Mb
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installed size is  5.6Mb
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Package suggested but not available for checking: ‘brms’
Package unavailable to check Rd xrefs: ‘brms’
installed size is 18.7Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 114.4Mb
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/triptych.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
installed size is 20.4Mb
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installed size is 34.1Mb
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GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.3Mb
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
Package unavailable to check Rd xrefs: ‘fpc’
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathabx.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {microtype}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

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

Error: Vignette re-building failed.
Execution halted
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checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
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    libs   2.5Mb
GNU make is a SystemRequirements.
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installed size is 96.9Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package unavailable to check Rd xrefs: ‘twang’
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Package which this enhances but not available for checking: ‘sl3’
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No news entries found.
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No news entries found.
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GNU make is a SystemRequirements.
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installed size is  8.0Mb
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Running examples in ‘UKFE-Ex.R’ failed
The error most likely occurred in:

> ### Name: MonthlyStats
> ### Title: Monthly Statistics
> ### Aliases: MonthlyStats
> 
> ### ** Examples
> 
> # Get the mean flows for each month for the Thames at Kingston
> QMonThames <- MonthlyStats(ThamesPQ[,c(1,3)], Stat = mean,
+ ylab = "Discharge (m3/s)", main = "Thames at Kingston monthly mean flow", Plot = TRUE)
Error in MonthlyStats(ThamesPQ[, c(1, 3)], Stat = mean, ylab = "Discharge (m3/s)",  : 
  At least one month does not have the same number of years available as the others. This may be because you have at least one whole month missing (as opposed to a month of NA values for example). You need at least one time step within each month
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
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2023-11-27 06:51:56.302 R[14525:2096614800] XType: Using static font registry.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
2023-11-27 06:51:58.157 R[15369:2096616534] XType: Using static font registry.
2023-11-27 06:52:00.054 R[16081:2096617951] XType: Using static font registry.
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
2023-11-27 06:52:02.337 R[16881:2096619572] XType: Using static font registry.
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
2023-11-27 06:52:04.198 R[17365:2096620546] XType: Using static font registry.
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
2023-11-27 06:52:07.135 R[18482:2096622832] XType: Using static font registry.
2023-11-27 06:52:13.295 R[20905:2096627616] XType: Using static font registry.
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
2023-11-27 06:52:15.181 R[21482:2096628821] XType: Using static font registry.
2023-11-27 06:52:16.786 R[22130:2096630090] XType: Using static font registry.
2023-11-27 06:52:18.255 R[22695:2096631227] XType: Using static font registry.
2023-11-27 06:52:20.449 R[23405:2096632632] XType: Using static font registry.
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.
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘adespatial’
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checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
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installed size is 39.3Mb
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Problems with news in ‘NEWS.md’:
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Packages suggested but not available for checking: 'vaers', 'vaersND'
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No news entries found.
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
installed size is  6.6Mb
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checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
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Missing link or links in documentation object 'amlbinomial.Rd':
  ‘[VGAMdata]{alaplace1}’

Missing link or links in documentation object 'amlexponential.Rd':
  ‘[VGAMdata]{alaplace1}’

Missing link or links in documentation object 'amlnormal.Rd':
  ‘[VGAMdata]{alaplace1}’

Missing link or links in documentation object 'amlpoisson.Rd':
  ‘[VGAMdata]{alaplace1}’

Missing link or links in documentation object 'extlogF.UC.Rd':
  ‘[VGAMdata]{dalap}’

Missing link or links in documentation object 'extlogF1.Rd':
  ‘[VGAMdata]{alaplace1}’ ‘[VGAMdata]{dalap}’

Missing link or links in documentation object 'grc.Rd':
  ‘[VGAMdata]{alaplace2}’

Missing link or links in documentation object 'laplace.Rd':
  ‘[VGAMdata]{alaplace2}’

Missing link or links in documentation object 'lms.bcn.Rd':
  ‘[VGAMdata]{alaplace1}’

Missing link or links in documentation object 'simulate.vlm.Rd':
  ‘[VGAMdata]{alaplace1}’ ‘[VGAMdata]{alaplace2}’
  ‘[VGAMdata]{triangle}’

Missing link or links in documentation object 'triangleUC.Rd':
  ‘[VGAMdata]{triangle}’

Missing link or links in documentation object 'wald.stat.Rd':
  ‘[VGAMdata]{alaplace1}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
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Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
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GNU make is a SystemRequirements.
installed size is 63.9Mb
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No news entries found.
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    vortexRdata pre-1.0.3
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checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
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installed size is  9.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 117.8Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘prepr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
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Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.8Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.7Mb
  sub-directories of 1Mb or more:
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    libs  10.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘org.Mm.eg.db’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
installed size is 94.2Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 58.8Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘classInt’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘wordnetDicts’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
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Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘wmtsa’
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘ROTS’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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Package suggested but not available for checking: ‘preprocessCore’
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
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installed size is 14.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 54.4Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 32.6Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
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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
Package suggested but not available for checking: ‘nlmixr2’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
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installed size is 25.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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installed size is 41.4Mb
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GNU make is a SystemRequirements.
installed size is 40.3Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
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Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 41.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/getting-started.Rmd’
   ‘vignettes/project-owners.Rmd’
(Is a VignetteBuilder field missing?)
Package suggested but not available for checking: ‘rJava’
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: \_
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/zoomerjoin.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘partitions’
installed size is 10.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.0Mb
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'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
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Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
installed size is  6.6Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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installed size is  6.9Mb
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installed size is  9.4Mb
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
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A package should be listed in only one of these fields.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package which this enhances but not available for checking: 'asreml'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
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checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'metaboliteIDmapping'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.3Mb
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
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installed size is  7.1Mb
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installed size is  6.0Mb
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sort_asap: no visible global function definition for 'sort_by'
Undefined global functions or variables:
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Package suggested but not available for checking: 'arcgisbinding'
Package suggested but not available for checking: 'ArchaeoData'
Found the following significant warnings:
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  Warning: read_chronomodel.Rd:36: unknown macro '\abbr'
  Warning: read_oxcal.Rd:27: unknown macro '\abbr'
See 'd:/Rcompile/CRANpkg/local/4.3/ArchaeoPhases.Rcheck/00install.out' for details.
prepare_Rd: read_bcal.Rd:27: unknown macro '\abbr'
prepare_Rd: read_chronomodel.Rd:36: unknown macro '\abbr'
prepare_Rd: read_oxcal.Rd:27: unknown macro '\abbr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.3Mb
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Packages suggested but not available for checking:
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installed size is  5.4Mb
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 44.7Mb
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installed size is 14.3Mb
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checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'asteRiskData'
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.3Mb
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'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
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checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
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Package suggested but not available for checking: 'lixoftConnectors'
installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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installed size is  7.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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installed size is  5.5Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'fdpbandsdata'
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
installed size is  9.4Mb
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installed size is  6.0Mb
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installed size is  7.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Earlier versions
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
installed size is  8.6Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
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checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
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checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
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checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
installed size is  7.0Mb
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GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
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Package suggested but not available for checking: 'INLA'
installed size is  7.3Mb
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GNU make is a SystemRequirements.
installed size is  7.7Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is 13.9Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.2Mb
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'library' or 'require' call not declared from: 'x'
installed size is  6.6Mb
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installed size is  6.2Mb
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installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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    doc   3.8Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.2Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.1Mb
    libs   1.6Mb
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.4Mb
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
installed size is 149.2Mb
  sub-directories of 1Mb or more:
    include  148.1Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'ffbase'
Package suggested but not available for checking: 'INLA'
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    3.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    help   2.6Mb
    libs   1.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      1.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.0Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning: 'blandr.output.text' is deprecated.
  Warning: 'blandr.output.text' is deprecated.
  Warning: 'blandr.output.text' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       5.3Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
Packages suggested but not available for checking:
  'adiposerefdata', 'musclerefdata'
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
    libs   1.2Mb
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      29.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'brea.Rmd' using rmarkdown

Quitting from lines 303-305 [unnamed-chunk-18] (brea.Rmd)
Error: processing vignette 'brea.Rmd' failed with diagnostics:
package 'MASS' must be installed
--- failed re-building 'brea.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R     3.8Mb
    doc   3.6Mb
Package suggested but not available for checking: 'glmmADMB'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/BRugs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    components   1.0Mb
    fonts        2.9Mb
    lib          4.9Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
pairwise.matrix: no visible global function definition for '%||%'
Undefined global functions or variables:
  %||%
Running examples in 'bullseye-Ex.R' failed
The error most likely occurred in:

> ### Name: pair_ace
> ### Title: Alternating conditional expectations correlation
> ### Aliases: pair_ace
> 
> ### ** Examples
> 
>  pair_ace(iris)
Error in rownames(m) %||% paste0("V", seq_along(xindex)) : 
  could not find function "%||%"
Calls: pair_ace -> pairwise -> pairwise.data.frame -> pairwise.matrix
Execution halted
Error(s) in re-building vignettes:
--- re-building 'calc_pairwise.Rmd' using rmarkdown

Quitting from lines 44-46 [unnamed-chunk-3] (calc_pairwise.Rmd)
Error: processing vignette 'calc_pairwise.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building 'calc_pairwise.Rmd'

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

Quitting from lines 57-62 [corrplot_assoc] (integrating.Rmd)
Error: processing vignette 'integrating.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building 'integrating.Rmd'

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

Quitting from lines 52-53 [unnamed-chunk-3] (vis_pairwise.Rmd)
Error: processing vignette 'vis_pairwise.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building 'vis_pairwise.Rmd'

SUMMARY: processing the following files failed:
  'calc_pairwise.Rmd' 'integrating.Rmd' 'vis_pairwise.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   9.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    entry_level                 1.7Mb
    virtual_patient_simulator   3.1Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rnaturalearthhires'
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    www  12.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc  19.9Mb
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'rkeops'
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
GNU make is a SystemRequirements.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc   16.4Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Error(s) in re-building vignettes:
--- re-building 'atp_calculation.Rmd' using rmarkdown
File mito_glyco_tests.png not found in resource path
Error: processing vignette 'atp_calculation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'atp_calculation.Rmd'

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

SUMMARY: processing the following file failed:
  'atp_calculation.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:
    data   3.2Mb
    doc    2.0Mb
    libs   1.7Mb
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'chain_glm.Rmd' using rmarkdown

Quitting from lines 173-174 [glm1_3] (chain_glm.Rmd)
Error: processing vignette 'chain_glm.Rmd' failed with diagnostics:
package 'MASS' must be installed
--- failed re-building 'chain_glm.Rmd'

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

SUMMARY: processing the following file failed:
  'chain_glm.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  9.1Mb
  sub-directories of 1Mb or more:
    R     5.0Mb
    doc   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'darts'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'countreg'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   2.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'entab'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R         1.8Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'pwalign'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    extdata  48.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tobit1'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/CNVScope.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'PopGenome'
Package suggested but not available for checking: 'disttree'
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    help   1.9Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc   9.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.0Mb
Unexported object imported by a ':::' call: 'crayon:::mypaste'
  See the note in ?`:::` about the use of this operator.
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java   6.7Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'CAM'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer3'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'EnsDb.Hsapiens.v86'
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc   11.7Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    libs   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.5Mb
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Packages required and available but unsuitable versions:
  'stats', 'tools', 'utils'

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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.3Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: jpegReport.Rd:22: unknown macro '\abbr'
  Warning: jpegReport.Rd:50: unknown macro '\abbr'
  Warning: jpegReport.Rd:53: unknown macro '\abbr'
  Warning: jpegReport.Rd:56: unknown macro '\abbr'
  Warning: jpegReport.Rd:58: unknown macro '\abbr'
  Warning: jpegReport.Rd:62: unknown macro '\abbr'
  Warning: pdfReport.Rd:101: unknown macro '\abbr'
  Warning: pngReport.Rd:22: unknown macro '\abbr'
  Warning: pngReport.Rd:50: unknown macro '\abbr'
  Warning: pngReport.Rd:53: unknown macro '\abbr'
  Warning: pngReport.Rd:55: unknown macro '\abbr'
  Warning: pngReport.Rd:59: unknown macro '\abbr'
  Warning: readReportTable.Rd:35: unknown macro '\abbr'
  Warning: readReportTable.Rd:167: unknown macro '\abbr'
  Warning: scanReport.Rd:45: unknown macro '\abbr'
  Warning: scanReport.Rd:60: unknown macro '\abbr'
  Warning: scanReport.Rd:61: unknown macro '\abbr'
  Warning: scanReport.Rd:162: unknown macro '\abbr'
See 'd:/Rcompile/CRANpkg/local/4.3/D4TAlink.light.Rcheck/00install.out' for details.
prepare_Rd: jpegReport.Rd:22: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:50: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:53: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:56: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:58: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:62: unknown macro '\abbr'
prepare_Rd: pdfReport.Rd:101: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:22: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:50: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:53: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:55: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:59: unknown macro '\abbr'
prepare_Rd: readReportTable.Rd:35: unknown macro '\abbr'
prepare_Rd: readReportTable.Rd:167: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:45: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:60: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:61: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:162: unknown macro '\abbr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
LazyData DB of 5.1 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SASxport'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [133s]
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(dawaR)
  ## {dawaR} provides data from the Danish Agency of Climate Data
  ## Terms and conditions apply.
  ## Read more at: https://dawadocs.dataforsyningen.dk/dok/om#vilkaar
  > 
  > test_check("dawaR")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 36 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • On CRAN (17): 'test-2-get_data-sections.R:2:3',
    'test-3-get_map_data-sections.R:2:3', 'test-afstemningsomraader.R:3:3',
    'test-afstemningsomraader.R:21:3', 'test-autocomplete.R:3:3',
    'test-base_api.R:18:3', 'test-get_data.R:30:3',
    'test-get_map_data-kommuner.R:2:3', 'test-get_map_data-politikredse.R:2:3',
    'test-get_map_data-regioner.R:2:3', 'test-get_map_data-vote.R:2:3',
    'test-get_map_data.R:3:3', 'test-reverse.R:3:3', 'test-status_check.R:20:3',
    'test-status_check.R:20:3', 'test-status_check.R:20:3',
    'test-status_check.R:20:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-status_check.R:16:3'): Status check function parses the rss feed and returns a dataframe if specified ──
  `observed_df` (`actual`) not equal to `expected_df` (`expected`).
  
  `actual$status[[6]]`:   "Down"
  `expected$status[[6]]`: "OK"  
  
  `actual$status[[7]]`:   "Down"
  `expected$status[[7]]`: "OK"  
  
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 36 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'BRugs'
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   2.2Mb
    libs   1.9Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.N' '.Nmiss' '.Q1' '.Q3' '.factorN' '.factorNmiss' '.factorQ1'
  '.factorQ3' '.factormax' '.factormean' '.factormedian' '.factormin'
  '.factorsd' '.max' '.mean' '.median' '.min' '.sd'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
    libs   1.2Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Error(s) in re-building vignettes:
--- re-building 'custom.Rmd' using rmarkdown
--- finished re-building 'custom.Rmd'

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

--- re-building 'engine.Rmd' using rmarkdown
Warning in gsub(this, knitr::sew(tmp), code) :
  TRE pattern compilation error 'Invalid back reference'

Quitting from lines 170-171 [unnamed-chunk-11] (engine.Rmd)
Error: processing vignette 'engine.Rmd' failed with diagnostics:
invalid regular expression 'D:\temp\2024_12_04_01_50_01_26701\RtmpYnq8hl\file16708e647e60.png', reason 'Invalid back reference'
--- failed re-building 'engine.Rmd'

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

Quitting from lines 56-62 [unnamed-chunk-5] (objects.Rmd)
Error: processing vignette 'objects.Rmd' failed with diagnostics:
invalid regular expression 'D:\temp\2024_12_04_01_50_01_26701\RtmpQVvLCP\file661847a61f7d.png', reason 'Invalid back reference'
--- failed re-building 'objects.Rmd'

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

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

SUMMARY: processing the following files failed:
  'engine.Rmd' 'objects.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:
    data          1.8Mb
    htmlwidgets   3.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'signatureSearchData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'dhis2r.Rmd' using rmarkdown

Quitting from lines 48-50 [unnamed-chunk-3] (dhis2r.Rmd)
Error: processing vignette 'dhis2r.Rmd' failed with diagnostics:
HTTP 404 Not Found.
--- failed re-building 'dhis2r.Rmd'

SUMMARY: processing the following file failed:
  'dhis2r.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'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
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
Package which this enhances but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BOLTSSIRR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.6Mb
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   1.7Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    data      2.0Mb
    extdata   2.3Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New features
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Missing or unexported object: 'visOmopResults::optionsVisOmopTable'
Running examples in 'DrugUtilisation-Ex.R' failed
The error most likely occurred in:

> ### Name: defaultTableOptions
> ### Title: Additional arguments for the table functions.
> ### Aliases: defaultTableOptions
> 
> ### ** Examples
> 
> {
+   defaultTableOptions()
+ }
Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'create_cohorts.Rmd' using rmarkdown
--- finished re-building 'create_cohorts.Rmd'

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

Quitting from lines 277-278 [unnamed-chunk-9] (drug_utilisation.Rmd)
Error: processing vignette 'drug_utilisation.Rmd' failed with diagnostics:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
--- failed re-building 'drug_utilisation.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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The following files should probably not be installed:
  'econet.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/ECOSolveR.Rcheck/00install.out' for details.
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  Cannot extract version info from the following section titles:
    TODO:
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Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(erfe)
  > 
  > test_check("erfe")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dexpectilizeVecR.R:11:3'): de-expectilize a vector works ───────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'vctrs'
  Backtrace:
      ▆
   1. ├─testthat::expect_vector(out, size = length(sim_panel_data$pred1)) at test-dexpectilizeVecR.R:11:3
   2. │ └─base::tryCatch(...)
   3. │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   4. │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5. │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   6. └─base::loadNamespace(x)
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base (local) withOneRestart(expr, restarts[[1L]])
   9.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
  Error: Test failures
  Execution halted
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CCRR: no visible global function definition for '%||%'
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Undefined global functions or variables:
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  Cannot extract version info from the following section titles:
    minor changes
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.run: no visible binding for global variable 'init'
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Undefined global functions or variables:
  init run
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GNU make is a SystemRequirements.
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installed size is  9.2Mb
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installed size is  5.1Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/fdrDiscreteNull.Rcheck/00install.out' for details.
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installed size is  5.5Mb
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Package suggested but not available for checking: 'gridlayout'
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Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
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checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
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installed size is  7.1Mb
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installed size is  5.0Mb
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GNU make is a SystemRequirements.
installed size is  6.9Mb
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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'LazyData' is specified without 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
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Malformed Description field: should contain one or more complete sentences.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
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Problems with news in 'NEWS.md':
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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Package suggested but not available for checking: 'RandomFields'
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'LazyData' is specified without a 'data' directory
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Problems with news in 'NEWS.md':
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checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
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Package suggested but not available for checking: 'dggrids'
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installed size is  5.2Mb
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
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Package suggested but not available for checking: 'gdxrrw'
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Package suggested but not available for checking: 'genderdata'
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GNU make is a SystemRequirements.
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No news entries found.
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No news entries found.
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Error(s) in re-building vignettes:
--- re-building 'geoAr_geofacet.Rmd' using rmarkdown
File figure/tucmap-1.png not found in resource path
Error: processing vignette 'geoAr_geofacet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_geofacet.Rmd'

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

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

SUMMARY: processing the following files failed:
  'geoAr_geofacet.Rmd' 'geoAr_leaflet.Rmd'

Error: Vignette re-building failed.
Execution halted
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installed size is  6.8Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'geomarocdata'
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/GeoModels.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'RandomFields'

Package which this enhances but not available for checking: 'INLA'
Malformed Description field: should contain one or more complete sentences.
installed size is  6.0Mb
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installed size is  7.3Mb
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Specified C++11: please drop specification unless essential
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installed size is  5.0Mb
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Package suggested but not available for checking: 'RGtk2'
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is 10.0Mb
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checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': 'scales:::censor'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'productplots:::bound'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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Package suggested but not available for checking: 'lixoftConnectors'
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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Problems with news in 'NEWS.md':
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
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GNU make is a SystemRequirements.
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installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Problems with news in 'NEWS.md':
No news entries found.
Packages suggested but not available for checking:
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GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
installed size is  6.3Mb
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 46.0Mb
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.6Mb
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Package suggested but not available for checking: 'cmdstanr'
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'LazyData' is specified without a 'data' directory
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installed size is  5.5Mb
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checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for 'gg' with
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Package suggested but not available for checking: 'doMC'
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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Package required but not available: 'EnsDb.Hsapiens.v75'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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'LazyData' is specified without a 'data' directory
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No news entries found.
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
    doc     4.0Mb
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.ga.breed' '.ga.fitness' '.ga.init' '.ga.mutate' '.ga.step'
  '.ga.weight'
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    2.5Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.4Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'colorfulVennPlot'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'HadoopStreaming'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.3Mb
html_describe_con: multiple local function definitions for 'g' with
  different formal arguments
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    4.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("hoardr")
  > test_check("hoardr")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 84 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-HoardClient.R:155:3'): HoardClient works when files exist ──────
  Error in `sub(attr(x, "cpath"), "", x[[i]]$file)`: invalid regular expression 'D:\temp\2024_12_04_01_50_01_26701\RtmpYrP7sU/R/test456', reason 'Invalid back reference'
  Backtrace:
       ▆
    1. ├─testthat::expect_output(print(deets1), "<cached files>") at test-HoardClient.R:155:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─testthat::capture_output_lines(code, print, width = width)
    5. │   │   └─testthat:::eval_with_output(code, print = print, width = width)
    6. │   │     ├─withr::with_output_sink(path, withVisible(code))
    7. │   │     │ └─base::force(code)
    8. │   │     └─base::withVisible(code)
    9. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   10. ├─base::print(deets1)
   11. └─hoardr:::print.cache_info(deets1)
   12.   ├─base::cat(...)
   13.   ├─base::paste0("  file: ", sub(attr(x, "cpath"), "", x[[i]]$file))
   14.   └─base::sub(attr(x, "cpath"), "", x[[i]]$file)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 84 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'hoardr_vignette.Rmd' using rmarkdown

Quitting from lines 91-92 [unnamed-chunk-10] (hoardr_vignette.Rmd)
Error: processing vignette 'hoardr_vignette.Rmd' failed with diagnostics:
invalid regular expression 'D:\temp\2024_12_04_01_50_01_26701\RtmpmoMYmP/R/foobar', reason 'Invalid back reference'
--- failed re-building 'hoardr_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'microViz'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
'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:
    data   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.3Mb
    help   1.1Mb
Specified C++14: please drop specification unless essential
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'hubExamples', 'hubVis'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'microViz'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SparkR'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   1.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'icd'
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8404:37: warning: ISO C++ forbids flexible array member 'Elements' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8667:22: warning: ISO C++ forbids flexible array member 'pEventLogRecords' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8673:13: warning: ISO C++ forbids flexible array member 'ulOffsets' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:196:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:197:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:198:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/processthreadsapi.h:130:47: warning: ISO C does not allow extra ';' outside of a function [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/rpcndr.h:451:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/urlmon.h:1333:24: warning: ISO C restricts enumerator values to range of 'int' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/urlmon.h:1745:25: warning: ISO C restricts enumerator values to range of 'int' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winioctl.h:359:11: warning: ISO C forbids zero-size array 'SerialNumber' [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.3/igraph.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.2Mb
    help   2.0Mb
    libs   6.4Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8404:37: warning: ISO C++ forbids flexible array member 'Elements' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8667:22: warning: ISO C++ forbids flexible array member 'pEventLogRecords' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8673:13: warning: ISO C++ forbids flexible array member 'ulOffsets' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/rpcndr.h:447:19: warning: ISO C++ forbids flexible array member 'Format' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/oaidl.h:548:37: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/oaidl.h:499:29: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.3/imager.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.3Mb
    libs     10.7Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.6Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'accdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc   9.7Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'surveyspec'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   3.3Mb
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
    libs   3.1Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'iucnrdata'
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'locClass'
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          11.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   4.0Mb
    help      1.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    i18n   6.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'remMap'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kanjistat.data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   7.8Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RGeostats'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: 'pwalign'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kadmin'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'using_latent2likert.Rmd' using rmarkdown
File man/figures/courses-grouped-min.png not found in resource path
Error: processing vignette 'using_latent2likert.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'using_latent2likert.Rmd'

SUMMARY: processing the following file failed:
  'using_latent2likert.Rmd'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.8Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   4.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'rsyslog'
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.7Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs       1.4Mb
    testdata   1.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R              1.4Mb
    doc-overview   2.2Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential