'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 107.8Mb
  sub-directories of 1Mb or more:
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installed size is 131.2Mb
  sub-directories of 1Mb or more:
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    libs  125.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
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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
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  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_mvord2.Rmd’ using rmarkdown
--- finished re-building ‘vignette_mvord2.Rmd’

--- re-building ‘vignette_mvord.Rnw’ using Sweave
Loading required package: minqa
Loading required package: BB
Loading required package: ucminf
Loading required package: dfoptim
Error: processing vignette 'vignette_mvord.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'vignette_mvord.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 'vignette_mvord.Rnw'

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

Error: Vignette re-building failed.
Execution halted
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 10.1Mb
  sub-directories of 1Mb or more:
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    libs   7.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
GNU make is a SystemRequirements.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
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
  sub-directories of 1Mb or more:
    libs   4.3Mb
Specified C++11: please drop specification unless essential
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’
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.
Package suggested but not available for checking: ‘DEXSeq’
Package unavailable to check Rd xrefs: ‘DEXSeq’
'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 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
'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: ‘rhdf5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rhdf5’
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
':::' call which should be '::': ‘lhs:::maximinLHS’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_ \_
checkRd: (-1) makeNetwork.Rd:31: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
installed size is 21.0Mb
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    doc    2.8Mb
    libs  17.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    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 200.7Mb
  sub-directories of 1Mb or more:
    libs  200.0Mb
GNU make is a SystemRequirements.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 40.0Mb
  sub-directories of 1Mb or more:
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installed size is  6.8Mb
  sub-directories of 1Mb or more:
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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 20.3Mb
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    libs  18.8Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  6.1Mb
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checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  7.6Mb
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Package suggested but not available for checking: ‘doMPI’
'LazyData' is specified without a 'data' directory
Running examples in ‘NMRphasing-Ex.R’ failed
The error most likely occurred in:

> ### Name: MPC_AAM
> ### Title: MPC_AAM
> ### Aliases: MPC_AAM
> 
> ### ** Examples
> 
> data("fdat")
> mpc_aam_phased1 <- MPC_AAM(fdat$frequency_domain)
Error in localMaximumSlidingWindow(x, winSize) : 
  DLL requires the use of native symbols
Calls: MPC_AAM ... getLocalMaximumCWT -> localMaximum -> localMaximumSlidingWindow
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘NMRphasing_vignette.rmd’ using rmarkdown

Quitting from lines 82-92 [unnamed-chunk-5] (NMRphasing_vignette.rmd)
Error: processing vignette 'NMRphasing_vignette.rmd' failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘NMRphasing_vignette.rmd’

SUMMARY: processing the following file failed:
  ‘NMRphasing_vignette.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  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'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
Specified C++11: please drop specification unless essential
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.1Mb
    mods   3.3Mb
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
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’
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 10.5Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
    libs   4.4Mb
'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  7.3Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs  16.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
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 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:
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installed size is 13.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.8Mb
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    libs   5.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   1.9Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Specified C++11: please drop specification unless essential
installed size is 99.2Mb
  sub-directories of 1Mb or more:
    libs  98.2Mb
'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
'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
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    data   5.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 45.9Mb
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    libs  44.0Mb
GNU make is a SystemRequirements.
installed size is 42.3Mb
  sub-directories of 1Mb or more:
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    libs  40.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rhdf5', 'Rhdf5lib'

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  5.5Mb
  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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.4Mb
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GNU make is a SystemRequirements.
installed size is 31.2Mb
  sub-directories of 1Mb or more:
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    share  10.2Mb
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'unary_ops':
  ‘log10.ProcessNode’ ‘log10.ProcessGraphParameter’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
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installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 200.9Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘openNLPmodels.en’
installed size is  5.8Mb
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installed size is  5.9Mb
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installed size is 11.7Mb
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installed size is  7.1Mb
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installed size is 37.3Mb
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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:
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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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
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
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.4Mb
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installed size is  5.6Mb
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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  8.6Mb
  sub-directories of 1Mb or more:
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installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
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S3 methods shown with full name in documentation object 'pamr-internal':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
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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’
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! 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:
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Error: Vignette re-building failed.
Execution halted
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S3 methods shown with full name in documentation object 'format.relation':
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The \usage entries for S3 methods should use the \method markup and not
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
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Package which this enhances but not available for checking: ‘ffbase’
Unknown package ‘ffbase’ in Rd xrefs
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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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Problems with news in ‘NEWS.md’:
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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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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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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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'LazyData' is specified without a 'data' directory
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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
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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
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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S3 methods shown with full name in documentation object 'internals':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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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: ‘spDataLarge’
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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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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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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
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'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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'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  7.3Mb
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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
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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  5.2Mb
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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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installed size is  5.8Mb
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Error(s) in re-building vignettes:
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--- 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
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'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
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installed size is 11.9Mb
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Packages suggested but not available for checking: 'xcms', 'MSnbase'
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Package suggested but not available for checking: ‘Spectra’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  7.5Mb
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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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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GNU make is a SystemRequirements.
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checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: 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
installed size is 21.6Mb
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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.
installed size is 55.0Mb
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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-arm64/results/4.3/Rblpapi.Rcheck/00install.out’ for details.
installed size is 44.2Mb
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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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S3 methods shown with full name in documentation object 'export.default':
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S3 methods shown with full name in documentation object 'export.listpoly':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘rrelaxiv’
'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
installed size is 13.4Mb
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Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
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checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
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Packages suggested but not available for checking:
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/Rcplex.Rcheck/00install.out’ for details.
installed size is 20.1Mb
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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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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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GNU make is a SystemRequirements.
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installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
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  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
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 14.3Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      5.1Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    include        2.0Mb
    jsonexamples   3.8Mb
    libs          11.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   1.1Mb
    libs      5.2Mb
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
'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 required but not available: ‘rhdf5’

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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘devAll’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
'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
'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
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    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
'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 19.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  15.4Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   5.0Mb
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
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   3.7Mb
'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
checkRd: (-1) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:46: Escaped LaTeX specials: \$
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checkRd: (-1) ena.plot.trajectory.Rd:38: Escaped LaTeX specials: \$
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checkRd: (-1) ena.plot.trajectory.Rd:42: 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
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.
'LazyData' is specified without 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:
    doc    1.6Mb
    libs   7.3Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  13.5Mb
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: \_ \_
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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  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs      3.6Mb
    swagger   1.4Mb
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs     22.7Mb
    models    1.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
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
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
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
'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  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
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 28.3Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
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 30.1Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs   22.8Mb
'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
'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: \&
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checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
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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
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  5.1Mb
  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 21.5Mb
  sub-directories of 1Mb or more:
    include   3.1Mb
    libs     17.7Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  23.8Mb
'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 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
'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  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
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 103.5Mb
  sub-directories of 1Mb or more:
    libs  102.7Mb
GNU make is a SystemRequirements.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/rlibkriging.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘reactome.db’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    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
'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  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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 136.8Mb
  sub-directories of 1Mb or more:
    libs  136.4Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is 84.1Mb
  sub-directories of 1Mb or more:
    libs  83.4Mb
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
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
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       1.2Mb
    minizinc   3.3Mb
Specified C++11: please drop specification unless essential
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installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs  38.0Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 61.8Mb
  sub-directories of 1Mb or more:
    libs  61.2Mb
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 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
GNU make is a SystemRequirements.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Package required but not available: ‘AnnotationHub’

Package suggested but not available for checking: ‘recount3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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:
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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:
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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 101.1Mb
  sub-directories of 1Mb or more:
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    libs     98.9Mb
'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 13.9Mb
  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
'LazyData' is specified without a 'data' directory
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.4Mb
Specified C++11: please drop specification unless essential
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
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
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 86.5Mb
  sub-directories of 1Mb or more:
    libs  85.8Mb
GNU make is a SystemRequirements.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Specified C++11: please drop specification unless essential
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
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 17.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
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GNU make is a SystemRequirements.
installed size is  5.8Mb
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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
Specified C++11: please drop specification unless essential
installed size is 20.8Mb
  sub-directories of 1Mb or more:
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'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:
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    data   2.7Mb
    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 13.5Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    libs   7.4Mb
Package suggested but not available for checking: ‘RandomFields’
installed size is 59.1Mb
  sub-directories of 1Mb or more:
    libs  57.9Mb
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  6.0Mb
  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:
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installed size is 10.3Mb
  sub-directories of 1Mb or more:
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    libs   6.3Mb
'LazyData' is specified without a 'data' directory
installed size is 47.6Mb
  sub-directories of 1Mb or more:
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installed size is  6.2Mb
  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
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   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /opt/R/arm64/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
  #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/RQuantLib.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
installed size is 103.3Mb
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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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
'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  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
'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.
installed size is 13.1Mb
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'LazyData' is specified without a 'data' directory
installed size is 27.4Mb
  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
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
Specified C++11: please drop specification unless essential
installed size is 10.0Mb
  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’
Specified C++11: please drop specification unless essential
installed size is 45.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 272.8Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 36.6Mb
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GNU make is a SystemRequirements.
installed size is 41.7Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 36.5Mb
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Specified C++11: please drop specification unless essential
installed size is 29.0Mb
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installed size is 22.3Mb
  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  6.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Gviz’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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    projects   2.9Mb
Specified C++11: please drop specification unless essential
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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installed size is 100.0Mb
  sub-directories of 1Mb or more:
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installed size is  7.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
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installed size is 29.9Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 59.5Mb
  sub-directories of 1Mb or more:
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Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  7.8Mb
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Specified C++11: please drop specification unless essential
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object 'printHTML.trackInfo':
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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.
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
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
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 45.3Mb
  sub-directories of 1Mb or more:
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matrixOps:
  function(e1, e2)
matrixOps.rvec:
  function(x, y)
See section ‘Generic functions and methods’ 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: ‘gpuR’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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installed size is 64.2Mb
  sub-directories of 1Mb or more:
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    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:
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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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'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'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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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  6.9Mb
  sub-directories of 1Mb or more:
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installed size is 16.8Mb
  sub-directories of 1Mb or more:
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installed size is 33.8Mb
  sub-directories of 1Mb or more:
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installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
installed size is 10.1Mb
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Specified C++14: please drop specification unless essential
installed size is 11.0Mb
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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
installed size is 16.1Mb
  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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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 36.5Mb
  sub-directories of 1Mb or more:
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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
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installed size is  7.2Mb
  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
Specified C++11: please drop specification unless essential
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
Specified C++11: please drop specification unless essential
installed size is 15.6Mb
  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 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 40.7Mb
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    libs  38.1Mb
Specified C++11: please drop specification unless essential
installed size is 10.2Mb
  sub-directories of 1Mb or more:
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    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
  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:
    libs   4.9Mb
installed size is  6.1Mb
  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
Package suggested but not available for checking: ‘FitARMA’
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
'library' or 'require' call to ‘progress’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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    libs   3.3Mb
GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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    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
  sub-directories of 1Mb or more:
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    libs   3.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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    libs   3.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
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    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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Packages suggested but not available for checking:
  'dittoSeq', 'DropletUtils', 'Nebulosa'
Packages unavailable to check Rd xrefs: ‘DropletUtils’, ‘Nebulosa’
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   3.1Mb
Packages suggested but not available for checking:
  'ontoProc', 'rrvgo', 'SingleCellSignalR'
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Package required but not available: ‘LoomExperiment’

Packages suggested but not available for checking:
  'scRNAseq', 'sceasy', 'SeuratDisk', 'SeuratWrappers',
  'zellkonverter', 'GEOfastq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘simplifyEnrichment’
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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’
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S3 methods shown with full name in documentation object 'plot':
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S3 methods shown with full name in documentation object 'predict':
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S3 methods shown with full name in documentation object 'summary':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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Package unavailable to check Rd xrefs: ‘infercnv’
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checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
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GNU make is a SystemRequirements.
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Package which this enhances but not available for checking: ‘glmGamPoi’
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Error(s) in re-building vignettes:
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--- 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:
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Error: Vignette re-building failed.
Execution halted
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Problems with news in ‘NEWS.md’:
No news entries found.
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installed size is 56.5Mb
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Specified C++11: please drop specification unless essential
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installed size is  9.7Mb
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GNU make is a SystemRequirements.
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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.
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Package unavailable to check Rd xrefs: ‘ArrayExpress’
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--- 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 bbm8): Font bbm8 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SEI_vignette.Rnw’

SUMMARY: processing the following file failed:
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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.
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installed size is 33.7Mb
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Error(s) in re-building vignettes:
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--- 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’:
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checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
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Problems with news in ‘NEWS.md’:
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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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installed size is  8.0Mb
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GNU make is a SystemRequirements.
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Specified C++14: please drop specification unless essential
installed size is 10.0Mb
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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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checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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installed size is  7.9Mb
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installed size is  5.8Mb
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installed size is 261.3Mb
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'LazyData' is specified without a 'data' directory
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installed size is 11.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
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installed size is  7.1Mb
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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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Package suggested but not available for checking: ‘cmdstanr’
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Packages unavailable to check Rd xrefs: ‘motifmatchr’, ‘TFBSTools’, ‘chromVAR’
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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
'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.
Package required but not available: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
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There are ::: calls to the package's namespace in its code. A package
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Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
Package suggested but not available for checking: ‘INLA’
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Problems with news in ‘NEWS.md’:
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Packages required but not available: 'HTSSIP', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
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installed size is  7.8Mb
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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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
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GNU make is a SystemRequirements.
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checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
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checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
Package required but not available: ‘rhdf5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Unknown package ‘InformationValue’ in Rd xrefs
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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’
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Error(s) in re-building vignettes:
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--- 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:
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Error: Vignette re-building failed.
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There are ::: calls to the package's namespace in its code. A package
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Malformed Description field: should contain one or more complete sentences.
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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’
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Package required but not available: ‘GWASTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
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There are ::: calls to the package's namespace in its code. A package
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S3 methods shown with full name in documentation object 'plot.predictions':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
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installed size is  5.1Mb
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Package suggested but not available for checking: ‘NLMR’
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Package suggested but not available for checking: ‘NLMR’
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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Unknown package ‘sparsebn’ in Rd xrefs
installed size is  5.2Mb
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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
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
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installed size is 30.6Mb
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'LazyData' is specified without a 'data' directory
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Package required but not available: ‘SpatialExperiment’

Packages suggested but not available for checking: 'rhdf5', 'HDF5Array'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
installed size is 54.7Mb
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Specified C++11: please drop specification unless essential
installed size is  6.3Mb
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installed size is  5.6Mb
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Specified C++11: please drop specification unless essential
installed size is 14.9Mb
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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  5.2Mb
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Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
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installed size is 13.7Mb
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Package suggested but not available for checking: ‘spDataLarge’
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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
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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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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
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checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
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installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Specified C++11: please drop specification unless essential
installed size is 16.4Mb
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installed size is  6.1Mb
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    libs   2.9Mb
'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’:
  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  7.7Mb
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installed size is 52.3Mb
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    libs  50.5Mb
'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  5.7Mb
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    data   5.3Mb
installed size is 12.4Mb
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    help   1.1Mb
    libs  10.0Mb
installed size is  8.7Mb
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installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
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installed size is 28.1Mb
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'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
installed size is 104.3Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    lsndata   2.3Mb
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘stacomir.Rmd’ using rmarkdown
Quitting from lines 302-324 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
duplicated values in No.pas
--- failed re-building ‘stacomir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 28.7Mb
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installed size is 48.8Mb
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installed size is 16.5Mb
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    lib       2.4Mb
GNU make is a SystemRequirements.
installed size is 90.0Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
Package suggested but not available for checking: ‘starsdata’
installed size is  6.3Mb
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    nc    1.7Mb
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
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installed size is  7.1Mb
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Package suggested but not available for checking: ‘snpStats’
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installed size is  9.4Mb
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    libs   5.3Mb
Package unavailable to check Rd xrefs: ‘snpStats’
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installed size is  5.0Mb
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installed size is  7.3Mb
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installed size is  7.8Mb
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Package suggested but not available for checking: ‘asreml’
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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.
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checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
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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  6.0Mb
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    libs   4.8Mb
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
installed size is  5.3Mb
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    data   1.7Mb
    libs   2.4Mb
Specified C++11: please drop specification unless essential
installed size is  7.6Mb
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installed size is  9.2Mb
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    doc    1.9Mb
    libs   6.4Mb
installed size is 28.3Mb
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
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    libs   7.1Mb
installed size is 10.4Mb
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    libs  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
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Package suggested but not available for checking: ‘StrathE2E2examples’
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installed size is  5.5Mb
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    libs   5.2Mb
installed size is 13.9Mb
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    libs  10.9Mb
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 34.7Mb
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installed size is  9.3Mb
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    doc    6.8Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
installed size is  5.6Mb
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checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    data   3.1Mb
    doc    1.3Mb
S3 methods shown with full name in documentation object 'size.penalize':
  ‘size.penalize’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
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installed size is  5.9Mb
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installed size is  7.7Mb
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Package suggested but not available for checking: ‘extraTrees’
Unknown package ‘extraTrees’ in Rd xrefs
Package suggested but not available for checking: ‘extraTrees’
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'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
surfaceSimulate : phytransform: no visible global function definition
  for ‘rescale’
Undefined global functions or variables:
  rescale
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
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installed size is 51.0Mb
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘gurobi’
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Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
installed size is  9.8Mb
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    data   2.3Mb
    doc    3.9Mb
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Unknown package ‘survJamda’ in Rd xrefs
installed size is  6.1Mb
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GNU make is a SystemRequirements.
installed size is  9.0Mb
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    libs   7.2Mb
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    Additional functions and data sets
    Amendments to functions
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    pre-release switchboard (2020 - 2021)
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GNU make is a SystemRequirements.
installed size is  5.0Mb
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    libs   4.9Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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installed size is  9.3Mb
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checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
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S3 methods shown with full name in documentation object 'designMatrices':
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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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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.
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GNU make is a SystemRequirements.
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Package required but not available: ‘EnhancedVolcano’

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 which this enhances but not available for checking: ‘fwelnet’
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Package suggested but not available for checking: ‘adaptiveGPCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is  5.9Mb
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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’
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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/triptych.Rcheck/00install.out’ for details.
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Malformed Title field: should not end in a period.
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GNU make is a SystemRequirements.
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There are ::: calls to the package's namespace in its code. A package
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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:
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Error: Vignette re-building failed.
Execution halted
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S3 methods shown with full name in documentation object 'tsibble-vctrs':
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  ‘vec_ptype2.yearmonth’ ‘vec_cast.yearquarter’
  ‘vec_ptype2.yearquarter’ ‘vec_cast.yearweek’ ‘vec_ptype2.yearweek’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.8Mb
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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
Package which this enhances but not available for checking: ‘sl3’
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GNU make is a SystemRequirements.
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installed size is  6.9Mb
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installed size is  5.4Mb
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Problems with news in ‘NEWS.md’:
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    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.
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'LazyData' is specified without a 'data' directory
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Unknown package ‘MortalityLaws’ in Rd xrefs
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GNU make is a SystemRequirements.
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See chapter ‘Writing R documentation files’ in the ‘Writing R
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
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Warning in initDict() :
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A namespace must be able to be loaded with just the base namespace
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Probably some imports need to be declared in the NAMESPACE file.
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/accrual.Rcheck/00install.out’ for details.
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Package required but not available: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Error(s) in re-building vignettes:
--- re-building ‘adivGuide.Rnw’ using Sweave

Attaching package: ‘phylobase’

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

    edges

Error: processing vignette 'adivGuide.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'adivGuide.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.12 \usepackage
                [all]{xy}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘adivGuide.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/AIUQ.Rcheck/00install.out’ for details.
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'library' or 'require' call to ‘network’ in package code.
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Malformed Title field: should not end in a period.
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Package required but not available: ‘ctmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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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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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Error(s) in re-building vignettes:
  ...
--- re-building ‘PPV_NPV.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘PPV_NPV.Rmd’

--- 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 71-82 [unnamed-chunk-2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Running examples in ‘BeeBDC-Ex.R’ failed
The error most likely occurred in:

> ### Name: interactiveMapR
> ### Title: Creates interactive html maps for species
> ### Aliases: interactiveMapR
> 
> ### ** Examples
> 
> OutPath_Figures <- tempdir()
> 
> interactiveMapR(
+ # occurrence data - start with entire dataset, filter down to these species
+ data = BeeBDC::bees3sp, # %>%
+   # Select only those species in the 100 randomly chosen
+   # dplyr::filter(scientificName %in% beeData_interactive$scientificName),
+   # Select only one species to map
+   # dplyr::filter(scientificName %in% "Agapostemon sericeus (Forster, 1771)"),
+ # Directory where to save files
+ outPath = paste0(OutPath_Figures, "/interactiveMaps_TEST"),
+ # lat long columns
+ lon = "decimalLongitude",
+ lat = "decimalLatitude",
+ # Occurrence dataset column with species names
+ speciesColumn = "scientificName",
+ # Which species to map - a character vector of names or "ALL"
+ # Note: "ALL" is defined AFTER filtering for country
+ speciesList = "ALL",
+ # studyArea
+ countryList = NULL, 
+ # Point jitter to see stacked points - jitters an amount in decimal degrees
+ jitterValue = 0.01,
+ # If TRUE, it will only map the .summary column. Otherwise, it will map .summary
+ # which will be over-written by countryOutliers and manualOutliers
+ onlySummary = TRUE,
+ excludeApis_mellifera = TRUE,
+ overWrite = TRUE,
+   # Colours for points which are flagged as TRUE, FALSE, countryOutlier, and customOutlier
+ pointColours = c("blue", "darkred","#ff7f00", "black")
+ )
Loading required namespace: htmlwidgets
Loading required namespace: leaflet
The column .expertOutlier was not found. One will be created with all values = TRUE.
Error in pandoc_self_contained_html(file, file) : 
  Saving a widget with selfcontained = TRUE requires pandoc. See here to learn more https://bookdown.org/yihui/rmarkdown-cookbook/install-pandoc.html
Calls: interactiveMapR -> <Anonymous> -> pandoc_self_contained_html
Execution halted
Running ‘testthat.R’ [40s/79s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  are planar
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 228 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-interactiveMapR.R:9:1'): (code run outside of `test_that()`) ───
  Error in `pandoc_self_contained_html(file, file)`: Saving a widget with selfcontained = TRUE requires pandoc. See here to learn more https://bookdown.org/yihui/rmarkdown-cookbook/install-pandoc.html
  Backtrace:
      ▆
   1. └─BeeBDC::interactiveMapR(...) at test-interactiveMapR.R:9:1
   2.   └─htmlwidgets::saveWidget(...)
   3.     └─htmlwidgets:::pandoc_self_contained_html(file, file)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 228 ]
  Error: Test failures
  Execution halted
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Note: skipping ‘betareg.Rnw’ due to unavailable dependencies: 'car'
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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    libs   5.0Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   6.1Mb
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is 170.5Mb
  sub-directories of 1Mb or more:
    include  170.4Mb
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
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    libs   4.6Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.8Mb
Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
installed size is  5.6Mb
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    data   5.2Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
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Package suggested but not available for checking: ‘RODBC’
Package suggested but not available for checking: ‘RODBC’

Package which this enhances but not available for checking: ‘leaps’
Specified C++14: please drop specification unless essential
installed size is  6.3Mb
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    extdata   1.9Mb
    libs      2.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
installed size is  7.3Mb
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installed size is  8.9Mb
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    libs   8.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gaston’
installed size is  8.9Mb
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      8.5Mb
installed size is  5.7Mb
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    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
'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
'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:
    libs  87.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   2.6Mb
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
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    libs   5.3Mb
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'select.cfs':
  ‘select.cfs’

S3 methods shown with full name in documentation object 'select.fast.filter':
  ‘select.fast.filter’

S3 methods shown with full name in documentation object 'select.forward.Corr':
  ‘select.forward.Corr’

S3 methods shown with full name in documentation object 'select.forward.wrapper':
  ‘select.forward.wrapper’

S3 methods shown with full name in documentation object 'select.inf.chi2':
  ‘select.inf.chi2’

S3 methods shown with full name in documentation object 'select.inf.gain':
  ‘select.inf.gain’

S3 methods shown with full name in documentation object 'select.inf.symm':
  ‘select.inf.symm’

S3 methods shown with full name in documentation object 'select.process':
  ‘select.process’

S3 methods shown with full name in documentation object 'select.relief':
  ‘select.relief’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
Package required but not available: ‘rhdf5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.2Mb
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    libs      2.8Mb
installed size is  6.1Mb
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    doc   5.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/biplotbootGUI.Rcheck/00install.out’ for details.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘colorspace’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘deldir’ ‘rgl’ ‘tcltk’ ‘tcltk2’ ‘tkrplot’
  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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
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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
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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
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    libs   6.3Mb
installed size is  6.7Mb
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    libs   6.6Mb
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 131.1Mb
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    testdata    1.4Mb
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  8.4Mb
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    data   3.5Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 34.0Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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installed size is 13.6Mb
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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:
    libs  176.7Mb
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.
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:
    libs  89.9Mb
GNU make is a SystemRequirements.
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
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    libs   6.5Mb
Packages suggested but not available for checking:
  'graph', 'Rgraphviz', 'qgraph'
'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
Package suggested but not available for checking: ‘sangerseqR’
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 12.9Mb
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installed size is 394.6Mb
  sub-directories of 1Mb or more:
    include   10.3Mb
    lib      383.9Mb
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  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
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:
    libs   5.4Mb
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.0Mb
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    data   4.4Mb
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
installed size is 43.7Mb
  sub-directories of 1Mb or more:
    libs  43.4Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'RGtk2', 'cairoDevice', 'car', 'mediation'
Packages unavailable to check Rd xrefs: ‘car’, ‘mediation’
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘phyloseq’

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: ‘breathteststan’
Package unavailable to check Rd xrefs: ‘breathteststan’
installed size is 32.9Mb
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    libs  32.7Mb
GNU make is a SystemRequirements.
S3 methods shown with full name in documentation object 'subset.int':
  ‘subset.int’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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    libs   2.4Mb
Package suggested but not available for checking: ‘cmdstanr’
installed size is  8.2Mb
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    R     3.3Mb
    doc   3.5Mb
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’
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    fonts   3.6Mb
    lib     4.9Mb
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
Specified C++11: please drop specification unless essential
installed size is 110.0Mb
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installed size is 12.5Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
installed size is  5.3Mb
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    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  6.2Mb
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    doc       2.3Mb
    extdata   3.4Mb
Running examples in ‘bulkAnalyseR-Ex.R’ failed
The error most likely occurred in:

> ### Name: DEanalysis
> ### Title: Perform differential expression (DE) analysis on an expression
> ###   matrix
> ### Aliases: DEanalysis DEanalysis_edger DEanalysis_deseq2
> 
> ### ** Examples
> 
> expression.matrix.preproc <- as.matrix(read.csv(
+   system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"), 
+   row.names = 1
+ ))[1:100, 1:4]
> 
> anno <- AnnotationDbi::select(
+   getExportedValue('org.Mm.eg.db', 'org.Mm.eg.db'),
+   keys = rownames(expression.matrix.preproc),
+   keytype = 'ENSEMBL',
+   columns = 'SYMBOL'
+ ) %>%
+   dplyr::distinct(ENSEMBL, .keep_all = TRUE) %>%
+   dplyr::mutate(NAME = ifelse(is.na(SYMBOL), ENSEMBL, SYMBOL))
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'select': there is no package called ‘org.Mm.eg.db’
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
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
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Package suggested but not available for checking: ‘vars’
installed size is 22.8Mb
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    libs  21.2Mb
'LazyData' is specified without a 'data' directory
installed size is 91.2Mb
  sub-directories of 1Mb or more:
    libs  88.9Mb
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 105.0Mb
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    libs  104.6Mb
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
installed size is 67.2Mb
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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: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
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    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
Package suggested but not available for checking: ‘batchelor’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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installed size is 11.6Mb
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installed size is  9.0Mb
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    R      2.0Mb
    libs   5.9Mb
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
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: ‘alr4’
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    www  12.1Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
'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
'LazyData' is specified without a 'data' directory
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  19.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc  37.7Mb
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   6.2Mb
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
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    R      2.3Mb
    libs   3.5Mb
installed size is 42.2Mb
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    libs  41.6Mb
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Specified C++11: please drop specification unless essential
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.2Mb
'LazyData' is specified without a 'data' directory
installed size is 149.7Mb
  sub-directories of 1Mb or more:
    libs  149.2Mb
GNU make is a SystemRequirements.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
Package which this enhances but not available for checking: ‘mirt’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.2Mb
Package unavailable to check Rd xrefs: ‘mirt’
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   9.8Mb
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
## 
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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--- re-building ‘clValid.Rnw’ using Sweave
Loading required package: cluster
Read 7 items

Attaching package: ‘BiocGenerics’

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    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

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Loading required package: RankAggreg
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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’:
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Malformed Description field: should contain one or more complete sentences.
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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
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Attaching package: ‘compare’

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

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GNU make is a SystemRequirements.
Running examples in ‘cpr-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_surface
> ### Title: Get Two-Dimensional Control Net and Surface from n-dimensional
> ###   Control Nets
> ### Aliases: get_surface
> 
> ### ** Examples
> 
> ## Extract the control net and surface from a cpr_cn object.
> a_cn <- cn(pdg ~ btensor(list(day, age), df = list(15, 3), order = list(3, 2)),
+            data = spdg)
> 
> cn_and_surface <- get_surface(a_cn, n = 50)
> str(cn_and_surface, max.level = 2)
List of 2
 $ cn     :'data.frame':	45 obs. of  3 variables:
  ..$ Var1: num [1:45] -1 -0.945 -0.837 -0.734 -0.629 ...
  ..$ Var2: num [1:45] 45.9 45.9 45.9 45.9 45.9 ...
  ..$ z   : num [1:45] 1.625 1.169 0.761 0.578 0.496 ...
 $ surface:'data.frame':	10000 obs. of  3 variables:
  ..$ Var1: num [1:10000] -1 -0.98 -0.96 -0.939 -0.919 ...
  ..$ Var2: num [1:10000] 45.9 45.9 45.9 45.9 45.9 ...
  ..$ z   : num [1:10000] 1.63 1.44 1.27 1.13 1.02 ...
> 
> par(mfrow = c(1, 2))
> with(cn_and_surface$cn,
+      plot3D::persp3D(unique(Var1),
+                      unique(Var2),
+                      matrix(z,
+                             nrow = length(unique(Var1)),
+                             ncol = length(unique(Var2))),
+                      main = "Control Net")
+      )
tcltk DLL is linked to '/opt/R/x86_64/lib/libtk8.6.dylib'
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
  call: fun(libname, pkgname)
  error: Tcl/Tk libraries are missing: install the Tcl/Tk component from the R installer
Execution halted
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  8.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.2Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
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 43.7Mb
  sub-directories of 1Mb or more:
    libs  43.6Mb
'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
Package suggested but not available for checking: ‘rhdf5’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/crqa.Rcheck/00install.out’ for details.
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
Error(s) in re-building vignettes:
--- re-building ‘crs.Rnw’ using Sweave
Registered S3 method overwritten by 'crs':
  method         from
  predict.gsl.bs np  
Categorical Regression Splines (version 0.15-37)
[vignette("crs_faq") provides answers to frequently asked questions]
--- finished re-building ‘crs.Rnw’

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

--- re-building ‘spline_primer.Rnw’ using Sweave
Registered S3 method overwritten by 'crs':
  method         from
  predict.gsl.bs np  
Categorical Regression Splines (version 0.15-37)
[vignette("crs_faq") provides answers to frequently asked questions]
Error: processing vignette 'spline_primer.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'spline_primer.tex' failed.
LaTeX errors:
! LaTeX Error: File `harvard.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘spline_primer.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘cryptoQuotes.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 52-58 [unnamed-chunk-4] (cryptoQuotes.Rmd)
Error: processing vignette 'cryptoQuotes.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘cryptoQuotes.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    doc    1.6Mb
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ctmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
S3 methods shown with full name in documentation object 'internals':
  ‘qr.gs’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Package required and available but unsuitable version: ‘IRanges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    doc    1.2Mb
    help   1.0Mb
    libs   4.6Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs  22.9Mb
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
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/CytoSimplex.Rcheck/00install.out’ for details.
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
Package suggested but not available for checking: ‘lme4’
'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
'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  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   4.0Mb
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:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Package suggested but not available for checking: ‘msa’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
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
Specified C++11: please drop specification unless essential
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  9.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.4Mb
S3 methods shown with full name in documentation object 'dbglm-inl':
  ‘dbglm.iteration’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘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
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
Packages suggested but not available for checking: 'WGCNA', 'impute'
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'EMD', 'astrochron'
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'tram', 'cotram'
Package unavailable to check Rd xrefs: ‘tram’
'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:
    libs   5.9Mb
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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  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  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
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  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: ‘Rdonlp2’
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘Rdonlp2’
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.N’ ‘.Nmiss’ ‘.Q1’ ‘.Q3’ ‘.factorN’ ‘.factorNmiss’ ‘.factorQ1’
  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
  ‘.factorsd’ ‘.max’ ‘.mean’ ‘.median’ ‘.min’ ‘.sd’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.8Mb
    help   2.3Mb
    libs   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
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'
Specified C++11: please drop specification unless essential
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.9Mb
'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    1.9Mb
    libs   3.9Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GOstats’
Packages suggested but not available for checking:
  'IHW', 'RNASeqPower', 'zFPKM'
Specified C++11: please drop specification unless essential
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  14.1Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'spaMM', 'glmmTMB'

Packages which this enhances but not available for checking:
  'rstan', 'BayesianTools'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'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
'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: ‘parallelDist’
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rhdf5', 'HDF5Array'
Package unavailable to check Rd xrefs: ‘HDF5Array’
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
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘INLA’
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
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
Specified C++11: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘discreteMTP’
Unknown package ‘discreteMTP’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
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
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Problems with news in ‘NEWS.md’:
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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
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checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
S3 methods shown with full name in documentation object 'add.joint.mean.many':
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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 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’:
  Cannot extract version info from the following section titles:
    New features
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘doMPI’
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Unknown package ‘broomExtra’ in Rd xrefs
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Package required but not available: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’

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GNU make is a SystemRequirements.
File ‘eaf/libs/eaf.so’:
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  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
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Compiled code should not call entry points which might terminate R nor
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See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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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,
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               {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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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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GNU make is a SystemRequirements.
S3 methods shown with full name in documentation object 'addDrug.Lexis':
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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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S3 methods shown with full name in documentation object 'summary.error_interval':
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S3 methods shown with full name in documentation object 'summary.measure':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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S3 methods shown with full name in documentation object 'ETAS-internal':
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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.
Packages suggested but not available for checking:
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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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Unknown package ‘iptools’ in Rd xrefs
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GNU make is a SystemRequirements.
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/extBatchMarking.Rcheck/00install.out’ for details.
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checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Factoshiny.Rcheck/00install.out’ for details.
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GNU make is a SystemRequirements.
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Error(s) in re-building vignettes:
--- re-building ‘comparison-packages.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 215-217 [univariate-mean-change-mosum] (comparison-packages.Rmd)
Error: processing vignette 'comparison-packages.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'tcltk', details:
  call: fun(libname, pkgname)
  error: Tcl/Tk libraries are missing: install the Tcl/Tk component from the R installer
--- failed re-building ‘comparison-packages.Rmd’

--- re-building ‘comparison-pelt.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘comparison-pelt.Rmd’

--- re-building ‘examples-advanced.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘examples-advanced.Rmd’

--- re-building ‘examples-introductory.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘examples-introductory.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: ‘coxKM’
installed size is  8.5Mb
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checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
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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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Package suggested but not available for checking: ‘NNLM’
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘DESeq2’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/fbati.Rcheck/00install.out’ for details.
installed size is  5.9Mb
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GNU make is a SystemRequirements.
installed size is  7.7Mb
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installed size is 10.9Mb
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Package suggested but not available for checking: ‘fields’
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Unexported object imported by a ':::' call: ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
installed size is  7.7Mb
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installed size is 36.7Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/fdaPDE.Rcheck/00install.out’ for details.
installed size is  5.0Mb
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Problems with news in ‘NEWS.md’:
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    New Stuff
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checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
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installed size is 36.3Mb
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Running ‘testthat.R’ [14s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  attr(,"class")
  [1] "gg"     "ggplot"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ilr.R:11:3'): clr plus summary works ───────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(phyloseq)`: there is no package called 'phyloseq'
  Backtrace:
      ▆
   1. └─base::library(phyloseq) at test-ilr.R:11:2
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
  Error: Test failures
  Execution halted
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Package required but not available: ‘rhdf5’

Package suggested but not available for checking: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package suggested but not available for checking: ‘diveRsity’
Unknown package ‘diveRsity’ in Rd xrefs
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
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Malformed Description field: should contain one or more complete sentences.
installed size is  5.2Mb
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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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Packages suggested but not available for checking:
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Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
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'LazyData' is specified without a 'data' directory
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installed size is  7.3Mb
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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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GNU make is a SystemRequirements.
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Error(s) in re-building vignettes:
--- re-building ‘standsurv.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 85-90 (standsurv.Rmd) 
Error: processing vignette 'standsurv.Rmd' failed with diagnostics:
there is no package called 'flexsurvcure'
--- failed re-building ‘standsurv.Rmd’

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

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

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

--- re-building ‘flexsurv-examples.Rnw’ using Sweave
Loading required package: survival
Forming integrated rmst function...
Forming integrated mean function...
Loading required package: TH.data
Loading required package: MASS

Attaching package: ‘TH.data’

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

    geyser

--- finished re-building ‘flexsurv-examples.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
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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  6.2Mb
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Package suggested but not available for checking: ‘minet’
Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
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Package required but not available: ‘RGN’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
'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: ‘Mcomp’
Package suggested but not available for checking: ‘RandomFields’
installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/frailtypack.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
Error(s) in re-building vignettes:
--- 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) :
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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)

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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.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘freevig.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Warning in xfun::prose_index(text) : Code fences are not balanced
Warning in prose_index(x) : Code fences are not balanced
Warning in xfun::prose_index(text) : Code fences are not balanced
--- finished re-building ‘freevig.Rmd’

--- re-building ‘freegroup.Rnw’ using Sweave
Loading required package: magrittr
Loading required package: magic
Loading required package: abind
Loading required package: plyr

Attaching package: ‘freegroup’

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

    id

Error: processing vignette 'freegroup.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'freegroup.tex' failed.
LaTeX errors:
! LaTeX Error: File `tikz-cd.sty' not found.

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l.67 \begin
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--- failed re-building ‘freegroup.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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installed size is  8.0Mb
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installed size is  6.7Mb
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installed size is 76.1Mb
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Packages suggested but not available for checking:
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Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is  9.9Mb
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GNU make is a SystemRequirements.
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installed size is 14.0Mb
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checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
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Malformed Description field: should contain one or more complete sentences.
S3 methods shown with full name in documentation object 'plot.funData':
  ‘plot.funData’

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘WGCNA’
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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)

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

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
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checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
Package suggested but not available for checking: ‘caret’
Package which this enhances but not available for checking: ‘doMPI’
installed size is  9.6Mb
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Specified C++14: please drop specification unless essential
installed size is 48.9Mb
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':::' call which should be '::': ‘graphics:::grid’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
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installed size is 67.1Mb
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GNU make is a SystemRequirements.
installed size is 60.6Mb
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installed size is  9.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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Specified C++11: please drop specification unless essential
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installed size is 16.7Mb
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gputools’
Error(s) in re-building vignettes:
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--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘paleofire’
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/gdalBindings.Rcheck/00install.out’ for details.
installed size is 283.5Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/gdalraster.Rcheck/00install.out’ for details.
installed size is 13.4Mb
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installed size is  5.2Mb
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Package suggested but not available for checking: ‘gdxrrw’
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Error(s) in re-building vignettes:
  ...
--- re-building ‘geepack-manual.Rnw’ using Sweave
Loading required package: geepack
Error: processing vignette 'geepack-manual.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'geepack-manual.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

Type X to quit or <RETURN> to proceed,
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l.8 \usepackage
               [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘geepack-manual.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Package suggested but not available for checking: ‘genderdata’
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Package suggested but not available for checking: ‘muscle’
Package suggested but not available for checking: ‘rrvgo’
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installed size is 11.4Mb
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    libs   9.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xgboost’
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘simplifyEnrichment’
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
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
installed size is 31.5Mb
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Running examples in ‘geofi-Ex.R’ failed
The error most likely occurred in:

> ### Name: wfs_api
> ### Title: WFS API
> ### Aliases: wfs_api
> 
> ### ** Examples
> 
>   wfs_api(base_url = "http://geo.stat.fi/geoserver/wfs", 
+           queries = append(list("service" = "WFS", "version" = "1.0.0"), 
+                 list(request = "getFeature", 
+                      layer = "tilastointialueet:kunta4500k_2017")))
Requesting response from: http://geo.stat.fi/geoserver/wfs?service=WFS&version=1.0.0&request=getFeature&layer=tilastointialueet%3Akunta4500k_2017
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [geo.stat.fi] Resolving timed out after 10002 milliseconds
Calls: wfs_api ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘geofi_datasets.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘geofi_datasets.Rmd’

--- re-building ‘geofi_joining_attribute_data.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘geofi_joining_attribute_data.Rmd’

--- re-building ‘geofi_making_maps.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 211-259 [leaflet] (geofi_making_maps.Rmd)
Error: processing vignette 'geofi_making_maps.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘geofi_making_maps.Rmd’

--- re-building ‘geofi_spatial_analysis.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘geofi_spatial_analysis.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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
installed size is  6.4Mb
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Package suggested but not available for checking: ‘geomarocdata’
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installed size is  5.1Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/geoR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘geosphere.Rnw’ using Sweave
Loading required namespace: raster
Error: processing vignette 'geosphere.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'geosphere.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.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘geosphere.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 86.1Mb
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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’
Unknown package ‘RandomFields’ in Rd xrefs
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 31.0Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RGtk2’
'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 32.6Mb
  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
Package required but not available: ‘ggmsa’

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  8.2Mb
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    doc       3.0Mb
    extdata   1.6Mb
    libs      3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
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    libs   7.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
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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
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
'LazyData' is specified without a 'data' directory
installed size is 19.4Mb
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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
help_secondary: possible error in sec_axis(transform = help$reverse,
  ...): unused argument (transform = help$reverse)
'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   5.0Mb
installed size is 10.7Mb
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    R     2.0Mb
    doc   7.0Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'car', 'NetworkToolbox', 'NetworkComparisonTest'
Specified C++11: please drop specification unless essential
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': ‘scales:::censor’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘productplots:::bound’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MicrobiomeStat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.9Mb
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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: ‘lixoftConnectors’
installed size is  8.9Mb
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    help       2.4Mb
    testdata   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
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
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    doc    3.5Mb
    libs   2.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
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
installed size is  7.2Mb
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    doc   6.0Mb
Error(s) in re-building vignettes:
--- re-building ‘fully-customed.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘fully-customed.Rmd’

--- re-building ‘using-ggVennDiagram.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 73-81 [unnamed-chunk-4] (using-ggVennDiagram.Rmd)
Error: processing vignette 'using-ggVennDiagram.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘using-ggVennDiagram.Rmd’

--- re-building ‘using-new-shapes.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘using-new-shapes.Rmd’

--- re-building ‘venn-plot-with-more-than-four-sets.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘venn-plot-with-more-than-four-sets.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Unknown package ‘IC2’ in Rd xrefs
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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 63.9Mb
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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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checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
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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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'LazyData' is specified without a 'data' directory
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Malformed Description field: should contain one or more complete sentences.
installed size is  7.6Mb
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    R   7.0Mb
installed size is 28.6Mb
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Package suggested but not available for checking: ‘gvcm.cat’
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Unknown package ‘gvcm.cat’ in Rd xrefs
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,
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! Emergency stop.
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l.20 \usepackage
                {comment}^^M
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--- 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 ‘getting_started.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 13-18 [unnamed-chunk-1] (getting_started.Rmd)
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘getting_started.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Malformed Title field: should not end in a period.
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Package suggested but not available for checking: ‘monocle’
Package unavailable to check Rd xrefs: ‘monocle’
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GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
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GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++14: please drop specification unless essential
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'groc.fit':
  ‘groc.fit’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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Package required but not available: ‘org.Mm.eg.db’

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  6.0Mb
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Error(s) in re-building vignettes:
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--- re-building ‘HAC.Rnw’ using Sweave
Loading required package: copula
Warning in hac2nacopula(hac) : NAs introduced by coercion
Error: processing vignette 'HAC.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'HAC.tex' failed.
LaTeX errors:
! LaTeX Error: File `german.sty' not found.

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

! Emergency stop.
<read *> 
         
l.47 \selectlanguage
                    {english}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'HAC.Rnw'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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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’
installed size is  5.1Mb
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Package suggested but not available for checking: ‘Rmpi’
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checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
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checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
Error(s) in re-building vignettes:
--- re-building ‘HardyWeinberg.Rnw’ using Sweave
Loading required package: mice

Attaching package: 'mice'

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

    filter

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

    cbind, rbind

Loading required package: Rsolnp
Loading required package: nnet
Warning: Number of logged events: 1
Warning: Number of logged events: 1
Error: processing vignette 'HardyWeinberg.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'HardyWeinberg.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.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'HardyWeinberg.Rnw'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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GNU make is a SystemRequirements.
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installed size is 154.8Mb
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GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.5Mb
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    extdata   1.3Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
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installed size is  5.5Mb
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installed size is  8.2Mb
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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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installed size is 19.9Mb
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installed size is  5.2Mb
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installed size is  5.5Mb
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    data   1.5Mb
    doc    3.7Mb
installed size is  6.2Mb
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    doc   5.2Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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    libs   6.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
Specified C++11: please drop specification unless essential
installed size is 23.5Mb
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    doc    2.2Mb
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'LazyData' is specified without a 'data' directory
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Error(s) in re-building vignettes:
  ...
--- re-building ‘hetGP_vignette.Rnw’ using knitr

Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
Packages suggested but not available for checking:
  'marray', 'affy', 'Biobase', 'limma'
Package unavailable to check Rd xrefs: ‘limma’
Note: skipping ‘hexagon_binning.Rnw’ due to unavailable dependencies:
  'marray'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘RcmdrPlugin.HH’
S3 methods shown with full name in documentation object 'defunct':
  ‘anova.mean’ ‘print.glht.mmc.multicomp’ ‘coef.arima.HH’ ‘glht.mmc’
  ‘plot.odds.ratio’ ‘persp.plane’ ‘persp.floor’ ‘persp.back.wall.x’
  ‘persp.back.wall.y’ ‘persp.setup’ ‘plot.hov’ ‘plot.hov.bf’
  ‘plot.matchMMC’ ‘seqplot.forecast’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 11.8Mb
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    libs  11.3Mb
Package suggested but not available for checking: ‘geojsonio’
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
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    libs   3.9Mb
Specified C++11: please drop specification unless essential
installed size is  8.9Mb
  sub-directories of 1Mb or more:
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    libs        7.6Mb
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
installed size is 46.0Mb
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Package suggested but not available for checking: ‘colorfulVennPlot’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'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  6.9Mb
  sub-directories of 1Mb or more:
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    libs   4.9Mb
Package which this enhances but not available for checking: ‘RProtoBuf’
Package unavailable to check Rd xrefs: ‘RProtoBuf’
installed size is 49.7Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
installed size is  5.1Mb
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Specified C++11: please drop specification unless essential
installed size is  5.9Mb
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    libs   2.6Mb
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
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    libs   4.0Mb
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
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 60.4Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
installed size is  5.3Mb
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Specified C++11: please drop specification unless essential
installed size is 10.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 15.9Mb
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    libs  15.5Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
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installed size is  8.3Mb
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'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘hsphase.Rnw’ using Sweave
Loading required package: snowfall
Loading required package: snow
Error: processing vignette 'hsphase.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'hsphase.tex' failed.
LaTeX errors:
! LaTeX Error: File `fancybox.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \definecolor
                 {darkblue}{rgb}{0,0,0.5}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘hsphase.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 58.2Mb
  sub-directories of 1Mb or more:
    libs  57.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘HTSFilter’
Package required but not available: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    2.3Mb
    help   1.1Mb
installed size is 35.8Mb
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    libs  35.1Mb
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
'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  8.0Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘phyloseq’

Package suggested but not available for checking: ‘microViz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘hyd1d.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 82-209 [captions] (hyd1d.Rmd)
Error: processing vignette 'hyd1d.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘hyd1d.Rmd’

--- re-building ‘vignette_DE.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 84-209 [captions] (vignette_DE.Rmd)
Error: processing vignette 'vignette_DE.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘vignette_DE.Rmd’

SUMMARY: processing the following files failed:
  ‘hyd1d.Rmd’ ‘vignette_DE.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hydflood.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 85-158 [captions] (hydflood.Rmd)
Error: processing vignette 'hydflood.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘hydflood.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
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    extdata   5.5Mb
    libs      1.7Mb
installed size is  5.3Mb
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    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
Package suggested but not available for checking: ‘flowCore’
Package suggested but not available for checking: ‘jack’
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
installed size is  6.5Mb
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    doc   6.3Mb
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
installed size is  5.8Mb
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    doc    2.8Mb
    libs   1.8Mb
'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:
    data   4.4Mb
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SparkR’
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
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    data   6.1Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'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’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘icd’
installed size is  5.8Mb
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    data   5.6Mb
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 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
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
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  30.5Mb
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
  sub-directories of 1Mb or more:
    data   5.0Mb
S3 methods shown with full name in documentation object 'internals':
  ‘plot.page’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘IFCdata’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.2Mb
    help   2.1Mb
    libs  17.2Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         4.2Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 34.9Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.2Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     23.5Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs   12.3Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Specified C++11: please drop specification unless essential
Package unavailable to check Rd xrefs: ‘minfi’
'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’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Package suggested but not available for checking: ‘cmdstanr’
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/InterfaceqPCR.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  30.1Mb
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
Specified C++11: please drop specification unless essential
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Specified C++11: please drop specification unless essential
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   1.1Mb
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
Package suggested but not available for checking: ‘caret’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Note: skipping ‘tecator.Rmd’ due to unavailable dependencies: 'caret'
'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   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
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
S3 methods shown with full name in documentation object 'print.Item':
  ‘print.Item’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xcms’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
installed size is 64.4Mb
  sub-directories of 1Mb or more:
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    doc    2.3Mb
    libs  59.2Mb
GNU make is a SystemRequirements.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  15.1Mb
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: ‘gurobi’
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Package suggested but not available for checking: ‘AER’
Package unavailable to check Rd xrefs: ‘AER’
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.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
installed size is 60.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  55.7Mb
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  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
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 28.1Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
'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   1.1Mb
    libs   5.4Mb
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    i18n   6.5Mb
'LazyData' is specified without a 'data' directory
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installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.9Mb
Packages which this enhances but not available for checking:
  'remMap', 'mcen', 'RMTL'
'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
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    libs  14.9Mb
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    libs   3.8Mb
installed size is  5.7Mb
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    libs   4.7Mb
installed size is  6.7Mb
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    htmlwidgets   1.1Mb
    www           2.7Mb
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rhdf5’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
S3 methods shown with full name in documentation object 'bw.abram.temp':
  ‘bw.abram.temp’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 10.6Mb
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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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/kml3d.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/kml.Rcheck/00install.out’ for details.
S3 methods shown with full name in documentation object 'unlist.constr':
  ‘unlist.constr’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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Error(s) in re-building vignettes:
--- re-building ‘knot.Rnw’ using Sweave
Loading required package: knotR
Warning in plot.window(...) : "box" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "box" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "box" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "box" is not a graphical parameter
Warning in box(...) : "box" is not a graphical parameter
Warning in title(...) : "box" is not a graphical parameter
Error: processing vignette 'knot.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'knot.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 ‘knot.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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'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’
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installed size is  6.9Mb
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GNU make is a SystemRequirements.
installed size is  5.2Mb
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installed size is  9.9Mb
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checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘ergm.userterms’
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package ‘ergm.userterms’ in Rd xrefs
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
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Package unavailable to check Rd xrefs: ‘mixAK’
Unknown packages ‘clusterCrit’, ‘akmedoids’ in Rd xrefs
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checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
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Packages suggested but not available for checking: 'xcms', 'MSnbase'
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Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 25.9Mb
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    libs  24.5Mb
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'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
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checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
installed size is 17.7Mb
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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
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    extdata   1.1Mb
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installed size is 95.4Mb
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GNU make is a SystemRequirements.
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checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
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Package suggested but not available for checking: ‘fpc’
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checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
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    libs      8.8Mb
Packages suggested but not available for checking:
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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
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) Read.Rd:88: Escaped LaTeX specials: \#
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S3 methods shown with full name in documentation object 'BIC.threshold':
  ‘BIC.threshold’

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
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checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘pbkrtest’
Package unavailable to check Rd xrefs: ‘pbkrtest’
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GNU make is a SystemRequirements.
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checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
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Package unavailable to check Rd xrefs: ‘car’
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Specified C++11: please drop specification unless essential
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checkRd: (-1) SPSloess.Rd:71: Escaped LaTeX specials: \^ \^
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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
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Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’
Note: skipping ‘locuszoomr.Rmd’ due to unavailable dependencies:
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘rhdf5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/longitudinalData.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘RDRToolbox’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
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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
Error(s) in re-building vignettes:
  ...
--- re-building ‘lorentz.Rnw’ using Sweave
Loading required package: magrittr
Error: processing vignette 'lorentz.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'lorentz.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 ‘lorentz.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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'LazyData' is specified without a 'data' directory
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installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Packages suggested but not available for checking:
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checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
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Package unavailable to check Rd xrefs: ‘LSDsensitivity’
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Package unavailable to check Rd xrefs: ‘orthogene’
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GNU make is a SystemRequirements.
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Running examples in ‘madshapR-Ex.R’ failed
The error most likely occurred in:

> ### Name: dataset_visualize
> ### Title: Generate a web-based visual report for a dataset
> ### Aliases: dataset_visualize
> 
> ### ** Examples
> 
> {
+ 
+ # You can use our demonstration files to run examples
+ 
+ library(fs)
+ library(dplyr)
+ 
+ dataset <- madshapR_DEMO$dataset_TOKYO['height'] %>% slice(0)
+ dataset_summary <- madshapR_DEMO$`dataset_summary`
+ 
+ if(dir_exists(tempdir())) dir_delete(tempdir())
+ bookdown_path <- tempdir()
+ 
+ dataset_visualize(
+   dataset,
+   dataset_summary = dataset_summary,
+   bookdown_path = bookdown_path)
+   
+ # To open the file in browser, open 'bookdown_path/docs/index.html'. 
+ # Or use bookdown_open(bookdown_path) function.
+ 
+ }

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

Warning in verify_rstudio_version() :
  Please install or upgrade Pandoc to at least version 1.17.2; or if you are using RStudio, you can just install RStudio 1.0+.
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Package suggested but not available for checking: ‘quitte’
Package suggested but not available for checking: ‘SeqVarTools’
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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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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
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GNU make is a SystemRequirements.
installed size is  5.4Mb
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GNU make is a SystemRequirements.
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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
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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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Package suggested but not available for checking: ‘cmdstanr’
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    Initial version.
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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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GNU make is a SystemRequirements.
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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.
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Problems with news in ‘NEWS.md’:
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checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
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Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    "```"
  - "data <- read.table(\"test.txt\", header = TRUE, sep = \"\\t\")"
  - "```"
  - ""
  - "Next, the data will be normalized to the range of 0 to 1:"
  - ""
  + "plot(1:10)```"
  + ""
  + "Next, the data will be normalized to the range of 0 to 1:"
  + ""
  and 10 more ...
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 136 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'ropls', 'xcms'
Packages suggested but not available for checking: 'phyloseq', 'biomformat'
Running ‘testthat.R’ [22s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test--parsers_and_writers.R:202:3'): Converting to phyloseq ─────────
  <packageNotFoundError/error/condition>
  Error in `library(phyloseq)`: there is no package called 'phyloseq'
  Backtrace:
      ▆
   1. └─base::library(phyloseq) at test--parsers_and_writers.R:202:2
  
  [ FAIL 1 | WARN 1 | SKIP 3 | PASS 535 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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Packages suggested but not available for checking:
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GNU make is a SystemRequirements.
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No news entries found.
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S3 methods shown with full name in documentation object 'complete.miceadds':
  ‘complete.mids.nmi’ ‘complete.mids.1chain’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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Package required but not available: ‘phyloseq’

Package suggested but not available for checking: ‘dada2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
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Package suggested but not available for checking: ‘gurobi’
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Package required but not available: ‘InteractiveComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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':::' call which should be '::': ‘parallel:::detectCores’
  See the note in ?`:::` about the use of this operator.
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GNU make is a SystemRequirements.
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    Bug Fix
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    Optimization
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    Add New Function
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Running ‘testthat.R’ [92s/133s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_parallel.R:102:3'): data table threads are not changed in main session ──
  getDTthreads() (`actual`) not equal to 2L (`expected`).
  
    `actual`: 1
  `expected`: 2
  ── Failure ('test_parallel.R:105:3'): data table threads are not changed in main session ──
  getDTthreads() (`actual`) not equal to 2L (`expected`).
  
    `actual`: 1
  `expected`: 2
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 12612 ]
  Error: Test failures
  Execution halted
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Complete output:
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  > library(multinomineq)
  > test_check("multinomineq")
  
  Execution halted
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Error(s) in re-building vignettes:
--- re-building ‘vignette_mvord2.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘vignette_mvord2.Rmd’

--- re-building ‘vignette_mvord.Rnw’ using Sweave
Loading required package: minqa
Loading required package: BB
Loading required package: ucminf
Loading required package: dfoptim
Error: processing vignette 'vignette_mvord.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'vignette_mvord.tex' failed.
LaTeX errors:
! Font U/bbm/m/n/10.95=bbm10 at 10.95pt not loadable: Metric (TFM) file not found.
<to be read again> 
                   relax 
l.544 \end{align}
                 
! Emergency stop.
<to be read again> 
                   relax 
l.544 \end{align}
                 
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'vignette_mvord.Rnw'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Error(s) in re-building vignettes:
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--- 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:
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Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
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    Version (2018-01-22)
    Version  (2017-08-22)
    Version
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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':::' call which should be '::': ‘lhs:::maximinLHS’
  See the note in ?`:::` about the use of this operator.
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installed size is 41.0Mb
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    R              8.1Mb
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    include       10.3Mb
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installed size is  6.8Mb
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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
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Specified C++11: please drop specification unless essential
installed size is  8.0Mb
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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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installed size is  7.6Mb
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Running examples in ‘NMRphasing-Ex.R’ failed
The error most likely occurred in:

> ### Name: MPC_AAM
> ### Title: MPC_AAM
> ### Aliases: MPC_AAM
> 
> ### ** Examples
> 
> data("fdat")
> mpc_aam_phased1 <- MPC_AAM(fdat$frequency_domain)
Error in localMaximumSlidingWindow(x, winSize) : 
  DLL requires the use of native symbols
Calls: MPC_AAM ... getLocalMaximumCWT -> localMaximum -> localMaximumSlidingWindow
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘NMRphasing_vignette.rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 82-92 [unnamed-chunk-5] (NMRphasing_vignette.rmd)
Error: processing vignette 'NMRphasing_vignette.rmd' failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘NMRphasing_vignette.rmd’

SUMMARY: processing the following file failed:
  ‘NMRphasing_vignette.rmd’

Error: Vignette re-building failed.
Execution halted
'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
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/nnspat.Rcheck/00install.out’ for details.
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
Specified C++11: please drop specification unless essential
installed size is 10.8Mb
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    libs   5.1Mb
    mods   3.3Mb
'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
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installed size is  7.2Mb
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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’
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 10.5Mb
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    data   5.8Mb
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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
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 20.8Mb
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installed size is  5.2Mb
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘methods’

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 10.1Mb
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installed size is  6.3Mb
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installed size is 12.9Mb
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installed size is  5.9Mb
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installed size is  6.5Mb
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installed size is 10.5Mb
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Specified C++11: please drop specification unless essential
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Running ‘testthat.R’ [27s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(odpc)
  > 
  > test_check("odpc")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_old_ver.R:75:3'): Equality with stored lambda for DFM model for single component sparse odpc ──
  sparse_fit[[1]]$lambda not equal to `old_lambda_sparse_dfm`.
  1/1 mismatches
  [1] 0.462 - 1.38 == -0.913
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
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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
installed size is  6.8Mb
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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
installed size is  6.0Mb
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Package suggested but not available for checking: ‘cmdstanr’
installed size is 47.2Mb
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GNU make is a SystemRequirements.
installed size is 39.6Mb
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    libs  37.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rhdf5', 'Rhdf5lib'

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
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Package suggested but not available for checking: ‘spatstat’
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GNU make is a SystemRequirements.
installed size is  6.3Mb
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GNU make is a SystemRequirements.
installed size is 33.4Mb
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    share  10.2Mb
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'unary_ops':
  ‘log10.ProcessNode’ ‘log10.ProcessGraphParameter’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 10.7Mb
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installed size is  5.2Mb
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installed size is 204.5Mb
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GNU make is a SystemRequirements.
installed size is  7.2Mb
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Package suggested but not available for checking: ‘openNLPmodels.en’
installed size is  5.9Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘sop.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 219-222 [unnamed-chunk-18] (sop.Rmd)
Error: processing vignette 'sop.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘sop.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
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installed size is 11.0Mb
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installed size is  6.9Mb
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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’
manual.
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
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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’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.3Mb
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installed size is  5.6Mb
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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  5.8Mb
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'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘orgutils_examples.Rnw’ using Sweave
Loading required package: orgutils
Error: processing vignette 'orgutils_examples.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'orgutils_examples.tex' failed.
LaTeX errors:
! LaTeX Error: File `DejaVuSansMono.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'orgutils_examples.Rnw'

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

Error: Vignette re-building failed.
Execution halted
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installed size is 10.0Mb
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installed size is  5.2Mb
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    help   1.1Mb
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Package suggested but not available for checking: ‘Rcplex’
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Specified C++11: please drop specification unless essential
installed size is 16.2Mb
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GNU make is a SystemRequirements.
installed size is  6.8Mb
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    libs   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
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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:
    Changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
installed size is  5.6Mb
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Packages suggested but not available for checking:
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Packages which this enhances but not available for checking:
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'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'pamr-internal':
  ‘print.nsc’ ‘print.nsccv’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
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checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
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checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘Rmpi’
installed size is 16.2Mb
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'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  5.9Mb
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    libs   4.2Mb
Specified C++14: please drop specification unless essential
installed size is  7.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 47.2Mb
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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
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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:
  ‘partitionspaper.Rnw’ ‘scrabble.Rnw’ ‘setpartitions.Rnw’

Error: Vignette re-building failed.
Execution halted
S3 methods shown with full name in documentation object 'vec_cast.partial_time':
  ‘vec_cast.partial_time’

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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    data   1.5Mb
Package suggested but not available for checking: ‘anomalize’
installed size is  5.6Mb
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    doc   5.2Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  8.4Mb
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    R      6.2Mb
    help   2.1Mb
installed size is  6.4Mb
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installed size is  6.5Mb
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    help   3.3Mb
installed size is  6.5Mb
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installed size is  6.4Mb
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Package suggested but not available for checking: ‘kinship2’
S3 methods shown with full name in documentation object 'ped':
  ‘ped.markerNames’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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’
installed size is  6.8Mb
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    doc    1.1Mb
    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  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.5Mb
'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 22.7Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
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/pcds.Rcheck/00install.out’ for details.
Missing link or links in documentation object 'funsMuVarUndCS2D.Rd':
  ‘[pcds]{asy.varCS2D}’

Missing link or links in documentation object 'funsMuVarUndPE2D.Rd':
  ‘[pcds]{asy.varPE2D}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Running examples in ‘pcds.ugraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: ASedge.dens.tri
> ### Title: Edge density of the underlying or reflexivity graph of Arc Slice
> ###   Proximity Catch Digraphs (AS-PCDs) - one triangle case
> ### Aliases: ASedge.dens.tri
> 
> ### ** Examples
> 
> #\donttest{
> A<-c(1,1); B<-c(2,0); C<-c(1.5,2);
> Tr<-rbind(A,B,C);
> n<-10
> 
> set.seed(1)
> Xp<-pcds::runif.tri(n,Tr)$g
tcltk DLL is linked to '/opt/R/x86_64/lib/libtk8.6.dylib'
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
  call: fun(libname, pkgname)
  error: Tcl/Tk libraries are missing: install the Tcl/Tk component from the R installer
Execution halted
installed size is 140.0Mb
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GNU make is a SystemRequirements.
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/PDE.Rcheck/00install.out’ for details.
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
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    Fixed issues
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S3 methods shown with full name in documentation object 'qr.solve_exact':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
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Running ‘testthat.R’ [12s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test-icon.R:26:5'): orcid() makes orcid icon metadata ───────────────
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Backtrace:
      ▆
   1. ├─withr::with_tempdir(...) at test-icon.R:12:3
   2. │ └─withr::with_dir(tmp, code)
   3. │   └─base::force(code)
   4. └─plume (local) render(tmp_file, output_format = "rtf_document") at test-icon.R:26:5
   5.   └─rmarkdown (local) .fn(clean = FALSE, quiet = TRUE, ...)
   6.     └─rmarkdown::pandoc_available(required_pandoc, error = TRUE)
   7.       └─rmarkdown:::stop2(paste(msg, collapse = " "))
  
  [ FAIL 1 | WARN 0 | SKIP 29 | PASS 181 ]
  Error: Test failures
  Execution halted
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--- re-building ‘latent.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 225-229 (latent.Rmd)
Error: processing vignette 'latent.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘latent.Rmd’

--- re-building ‘projpred.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘projpred.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
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Package suggested but not available for checking: ‘rdt’
installed size is 25.0Mb
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installed size is  6.3Mb
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installed size is  6.3Mb
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installed size is  5.2Mb
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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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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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'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
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 27.5Mb
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installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
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installed size is 47.6Mb
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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
installed size is 33.2Mb
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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
'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) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) Ch0C-plot.cpd.PwrGSD.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
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
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
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Missing or unexported objects:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCBA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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S3 methods shown with full name in documentation object 'internals':
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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 81.7Mb
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'LazyData' is specified without a 'data' directory
installed size is 121.4Mb
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'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
installed size is  5.1Mb
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Package suggested but not available for checking: ‘spDataLarge’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
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installed size is 15.7Mb
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Specified C++11: please drop specification unless essential
installed size is  7.9Mb
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Packages suggested but not available for checking: 'glmmTMB', 'DHARMa'
S3 methods shown with full name in documentation object 'internals':
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The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object 'internals':
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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 11.0Mb
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installed size is 12.6Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is  8.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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installed size is 15.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 37.5Mb
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Specified C++11: please drop specification unless essential
installed size is  6.5Mb
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installed size is 11.8Mb
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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  8.0Mb
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installed size is 10.9Mb
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installed size is  9.9Mb
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installed size is 10.7Mb
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Package suggested but not available for checking: ‘quanteda.textmodels’
Package unavailable to check Rd xrefs: ‘quanteda.textmodels’
'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: ‘survey’
Package unavailable to check Rd xrefs: ‘survey’
installed size is 11.6Mb
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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
installed size is  7.1Mb
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Specified C++11: please drop specification unless essential
installed size is 13.1Mb
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'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
Package suggested but not available for checking: ‘bootmlm’
Packages suggested but not available for checking: 'caret', 'xgboost'
installed size is  5.1Mb
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'library' or 'require' call to ‘RDCOMClient’ in package code.
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  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.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
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installed size is 21.0Mb
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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 11.7Mb
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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 36.6Mb
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installed size is  5.8Mb
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Error(s) in re-building vignettes:
--- re-building ‘rainbow.Rnw’ using Sweave
Loading required package: MASS
Loading required package: pcaPP
Warning in fts(x, notchlow) :
  Please assign column name for the data matrix.
Warning in fts(x, notchupper) :
  Please assign column name for the data matrix.
Warning in fts(x, centercurve) :
  Please assign column name for the data matrix.
Warning in fts(x, centercurve) :
  Please assign column name for the data matrix.
Warning in fts(object$x, svdr[, , i]) :
  Please assign column name for the data matrix.
Warning in fts(object$x, svdr[, , i]) :
  Please assign column name for the data matrix.
Warning in fts(object$x, svdr[, , i]) :
  Please assign column name for the data matrix.
Warning in fts(object$x, svdrecon) :
  Please assign column name for the data matrix.
Error: processing vignette 'rainbow.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'rainbow.tex' failed.
LaTeX errors:
! LaTeX Error: File `animate.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 ‘rainbow.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 29.0Mb
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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
installed size is 11.5Mb
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installed size is 11.9Mb
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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
'LazyData' is specified without 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.
Error(s) in re-building vignettes:
--- re-building ‘fullpres.Rnw’ using Sweave
Loading required package: rngWELL
This is randtoolbox. For an overview, type 'help("randtoolbox")'.
Warning in sobol(10^3, 2, scrambling = 1) :
  scrambling is currently disabled.
Warning in sobol(10^3, 2, scrambling = 2) :
  scrambling is currently disabled.
Warning in coll.test(runif, 2^7, 2^10, 1, echo = FALSE) :
  p-values will be approximated in the presence of low expected collision number.
Warning in coll.test(congruRand, 2^8, 2^14, 1, echo = FALSE) :
  p-values will be approximated in the presence of low expected collision number.
Error: processing vignette 'fullpres.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'fullpres.tex' failed.
LaTeX errors:
! LaTeX Error: File `perpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.79 \MakePerPage
                 [1]{footnote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘fullpres.Rnw’

--- re-building ‘shortintro.Rnw’ using Sweave
Loading required package: rngWELL
This is randtoolbox. For an overview, type 'help("randtoolbox")'.
Warning in RNGkind("default") :
  someone corrupted the random-number generator: re-initializing
Error: processing vignette 'shortintro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'shortintro.tex' failed.
LaTeX errors:
! LaTeX Error: File `perpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.87 \MakePerPage
                 [1]{footnote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘shortintro.Rnw’

SUMMARY: processing the following files failed:
  ‘fullpres.Rnw’ ‘shortintro.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
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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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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required and available but unsuitable versions:
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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: ‘gurobi’
installed size is 16.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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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
installed size is 11.8Mb
  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
installed size is  6.7Mb
  sub-directories of 1Mb or more:
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installed size is 68.5Mb
  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 12.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is 10.6Mb
  sub-directories of 1Mb or more:
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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:
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    libs  10.7Mb
'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:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   3.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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    libs      3.8Mb
GNU make is a SystemRequirements.
installed size is 53.5Mb
  sub-directories of 1Mb or more:
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    libs  50.8Mb
GNU make is a SystemRequirements.
installed size is 57.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rhdf5’
'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:
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    libs   5.3Mb
installed size is 45.0Mb
  sub-directories of 1Mb or more:
    libs  43.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'export.default':
  ‘export.default’

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
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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 13.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
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  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcmdrPlugin.BWS1.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcmdrPlugin.BWS2.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcmdrPlugin.BWS3.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcmdrPlugin.DCCV.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcmdrPlugin.DCE.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcmdrPlugin.EZR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcmdrPlugin.FactoMineR.Rcheck/00install.out’ for details.
'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
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcmdrPlugin.TeachStat.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
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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:
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Package suggested but not available for checking: ‘conics’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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installed size is  7.6Mb
  sub-directories of 1Mb or more:
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Packages suggested but not available for checking:
  'ROntoTools', 'hgu133plus2.db', '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
Specified C++11: please drop specification unless essential
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    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
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 48.3Mb
  sub-directories of 1Mb or more:
    include  48.1Mb
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
  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 30.8Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     22.8Mb
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
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-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 14.2Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      4.9Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    include        2.0Mb
    jsonexamples   3.8Mb
    libs          12.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    include   1.1Mb
    libs      5.5Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘evolMap’
Unavailable namespace imported from by a ':::' call: ‘evolMap’
  See the note in ?`:::` about the use of this operator.
Package required but not available: ‘rhdf5’

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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘devAll’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘rDNAse.Rnw’ using Sweave
Loading required package: rDNAse
Error: processing vignette 'rDNAse.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'rDNAse.tex' failed.
LaTeX errors:
! LaTeX Error: File `tablefootnote.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘rDNAse.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'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   4.3Mb
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
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.7Mb
    libs   1.0Mb
'LazyData' is specified without 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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ReDaMoR.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 159-163 [unnamed-chunk-5] (ReDaMoR.Rmd)
Error: processing vignette 'ReDaMoR.Rmd' failed with diagnostics:
Failed to start chrome. Error: 
--- failed re-building ‘ReDaMoR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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
'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 18.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  14.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   3.7Mb
'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
checkRd: (-1) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:42: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
'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.
'LazyData' is specified without 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:
    doc    1.6Mb
    libs   7.1Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  13.5Mb
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
Specified C++11: please drop specification unless essential
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs     20.8Mb
    models    1.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
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
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
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 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
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
'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.
'LazyData' is specified without a 'data' directory
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 28.6Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs   24.8Mb
Error(s) in re-building vignettes:
--- re-building ‘WebGL.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘WebGL.Rmd’

--- re-building ‘demos.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 30-130 [unnamed-chunk-1] (demos.Rmd)
Error: processing vignette 'demos.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 ‘demos.Rmd’

--- re-building ‘deprecation.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘deprecation.Rmd’

--- re-building ‘pkgdown.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘pkgdown.Rmd’

--- re-building ‘rgl.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘rgl.Rmd’

--- re-building ‘transparency.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘transparency.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RGN.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
  sub-directories of 1Mb or more:
    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
'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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      3.2Mb
    extdata   1.3Mb
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
'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 20.9Mb
  sub-directories of 1Mb or more:
    include   3.1Mb
    libs     17.0Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  23.8Mb
'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 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
'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 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   17.0Mb
'LazyData' is specified without a 'data' directory
installed size is 106.7Mb
  sub-directories of 1Mb or more:
    libs  105.9Mb
GNU make is a SystemRequirements.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/rlibkriging.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘reactome.db’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'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
'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  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
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 125.7Mb
  sub-directories of 1Mb or more:
    libs  125.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is 66.7Mb
  sub-directories of 1Mb or more:
    libs  65.9Mb
GNU make is a SystemRequirements.
Running examples in ‘RmdConcord-Ex.R’ failed
The error most likely occurred in:

> ### Name: processConcordance
> ### Title: Get the concordance from the "datapos" values and record it in a
> ###   file.
> ### Aliases: processConcordance
> 
> ### ** Examples
> 
> # This example works on the file inst/sample/Sample.Rmd,
> # which should be a copy of the vignette Sample.Rmd.  This
> # is convenient because RStudio doesn't install vignettes by default.
> 
> # First, see the results without concordances:
> 
> library(RmdConcord)
> dir <- tempdir()
> intermediates <- tempfile()
> 
> infile <- system.file("sample/Sample.Rmd", package = "RmdConcord")
> outfile1 <- file.path(dir, "html_vignette.html")
> 
> rmarkdown::render(infile,
+                   intermediates_dir = intermediates,
+                   output_file = outfile1,
+                   quiet = TRUE)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: \&
Specified C++11: please drop specification unless essential
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
  sub-directories of 1Mb or more:
    libs  27.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rmonize.Rcheck/00install.out’ for details.
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 62.6Mb
  sub-directories of 1Mb or more:
    libs  62.0Mb
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 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
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  6.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    2.2Mb
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 102.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     99.9Mb
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
Package suggested but not available for checking: ‘ROptEst’
Package unavailable to check Rd xrefs: ‘ROptEst’
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R  12.1Mb
'LazyData' is specified without a 'data' directory
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.8Mb
Specified C++11: please drop specification unless essential
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Error(s) in re-building vignettes:
--- re-building ‘robflreg.Rnw’ using Sweave
Loading required package: fda
Loading required package: splines
Loading required package: fds
Loading required package: rainbow
Loading required package: MASS
Loading required package: pcaPP
Loading required package: RCurl
Loading required package: deSolve

Attaching package: ‘fda’

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

    matplot

Loading required package: robustbase
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-42. For overview type 'help("mgcv-package")'.
 fda.usc is running sequentially usign foreach package
 Please, execute ops.fda.usc() once to run in local parallel mode
 Deprecated functions: min.basis, min.np, anova.hetero, anova.onefactor, anova.RPm
 New functions: optim.basis, optim.np, fanova.hetero, fanova.onefactor, fanova.RPm
----------------------------------------------------------------------------------

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

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘robflreg.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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'
Package unavailable to check Rd xrefs: ‘ROptEst’
Package suggested but not available for checking: ‘robustbase’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
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 87.8Mb
  sub-directories of 1Mb or more:
    libs  87.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘ivgets’
Package unavailable to check Rd xrefs: ‘ivgets’
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
Specified C++11: please drop specification unless essential
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
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:
    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
Package suggested but not available for checking: ‘XLConnect’
'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 17.3Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'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  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
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
Specified C++11: please drop specification unless essential
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
'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
Package suggested but not available for checking: ‘RobLox’
Package unavailable to check Rd xrefs: ‘RobLox’
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    libs   7.5Mb
Package suggested but not available for checking: ‘RandomFields’
installed size is 60.8Mb
  sub-directories of 1Mb or more:
    libs  59.6Mb
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  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
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 52.1Mb
  sub-directories of 1Mb or more:
    libs  52.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
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
Specified C++11: please drop specification unless essential
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'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 99.3Mb
  sub-directories of 1Mb or more:
    libs  98.7Mb
'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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘robustbase’
Package unavailable to check Rd xrefs: ‘robustbase’
Packages suggested but not available for checking: 'fields', 'qgraph'
'LazyData' is specified without 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
'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.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
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’
Specified C++11: please drop specification unless essential
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  41.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 281.5Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.8Mb
    libs  274.0Mb
GNU make is a SystemRequirements.
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    libs  36.8Mb
GNU make is a SystemRequirements.
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib   27.1Mb
    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 37.8Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
Specified C++11: please drop specification unless essential
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs    1.9Mb
    swipl  21.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.4Mb
    help   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    rmarkdown  11.2Mb
GNU make is a SystemRequirements.
Running ‘test-all.R’ [1s/1s]
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-check-template.R:2:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-rjournal_article.R:2:3'): rjournal_article() is deprecated ─────
  Error: pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-rjournal_article.R:2:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 2 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘Gviz’
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 100.2Mb
  sub-directories of 1Mb or more:
    libs  98.5Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘intamap’
'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
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 56.1Mb
  sub-directories of 1Mb or more:
    libs  55.7Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.5Mb
Specified C++11: please drop specification unless essential
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object 'printHTML.trackInfo':
  ‘printHTML.trackInfo’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
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
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 45.4Mb
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matrixOps:
  function(e1, e2)
matrixOps.rvec:
  function(x, y)
See section ‘Generic functions and methods’ 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: ‘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.
S3 methods shown with full name in documentation object 'matmult':
  ‘%*%.rv’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
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
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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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Packages suggested but not available for checking:
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installed size is  7.0Mb
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Packages unavailable to check Rd xrefs: ‘BiocPkgTools’, ‘biocViews’
installed size is  6.4Mb
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    doc    3.9Mb
installed size is  5.1Mb
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Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘cranly’
installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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installed size is 16.0Mb
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installed size is 31.5Mb
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installed size is  7.0Mb
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installed size is  9.5Mb
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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
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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 14.8Mb
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installed size is 12.3Mb
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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
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
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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  7.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.8Mb
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installed size is 15.0Mb
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'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'
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: \$
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checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
installed size is 39.5Mb
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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  5.5Mb
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installed size is  6.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
'library' or 'require' call to ‘progress’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
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installed size is  5.2Mb
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GNU make is a SystemRequirements.
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
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installed size is  5.4Mb
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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
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
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'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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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Packages suggested but not available for checking:
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Packages unavailable to check Rd xrefs: ‘DropletUtils’, ‘Nebulosa’
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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    libs   3.0Mb
Packages suggested but not available for checking:
  'ontoProc', 'rrvgo', 'SingleCellSignalR'
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
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Package required but not available: ‘LoomExperiment’

Packages suggested but not available for checking:
  'scRNAseq', 'sceasy', 'SeuratDisk', 'SeuratWrappers',
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
'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: ‘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
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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S3 methods shown with full name in documentation object 'plot':
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S3 methods shown with full name in documentation object 'predict':
  ‘predict.discretization’ ‘predict.reject_infered’

S3 methods shown with full name in documentation object 'summary':
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The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
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checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'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
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
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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
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Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 10.0Mb
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    libs   9.1Mb
installed size is 57.8Mb
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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
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
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    R   8.6Mb
installed size is 19.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  14.3Mb
GNU make is a SystemRequirements.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
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    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’
Package required and available but unsuitable version: ‘OasisR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Packages suggested but not available for checking:
  'spdep', 'spgrass6', 'rgdal'
'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 33.7Mb
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    www  33.6Mb
'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.
Package which this enhances but not available for checking: ‘semPlot’
Package suggested but not available for checking: ‘rockchalk’
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘semtable.Rnw’ using Sweave
Error in FUN(X[[i]], ...) : getFiles fc dir "theme"does not exist
Loading required package: lavaan
This is lavaan 0.6-15
lavaan is FREE software! Please report any bugs.
Error: processing vignette 'semtable.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'semtable.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.6 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘semtable.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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  5.3Mb
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    R      2.2Mb
    libs   2.5Mb
Specified C++11: please drop specification unless essential
installed size is 22.8Mb
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    libs    21.1Mb
    models   1.6Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
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    data   2.3Mb
    libs   4.0Mb
GNU make is a SystemRequirements.
installed size is  6.4Mb
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    data   1.2Mb
    libs   4.3Mb
Specified C++14: please drop specification unless essential
installed size is  9.4Mb
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    libs   8.1Mb
Specified C++11: please drop specification unless essential
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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 19.4Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
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
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    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 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'HDF5Array', 'BPCells'
Packages suggested but not available for checking:
  'BPCells', 'monocle', 'presto'
installed size is 10.5Mb
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    R      2.1Mb
    libs   7.5Mb
'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   7.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sf.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package unavailable to check Rd xrefs: ‘tripack’
installed size is 11.6Mb
  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  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is  7.2Mb
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    R      2.0Mb
    data   1.0Mb
    doc    3.8Mb
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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There are ::: calls to the package's namespace in its code. A package
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Packages required but not available: 'HTSSIP', 'phyloseq'

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manual.
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Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
installed size is  7.1Mb
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Package unavailable to check Rd xrefs: ‘caret’
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/slr.Rcheck/00install.out’ for details.
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GNU make is a SystemRequirements.
Package required but not available: ‘rhdf5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Unknown package ‘InformationValue’ in Rd xrefs
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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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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/smovie.Rcheck/00install.out’ for details.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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S3 methods shown with full name in documentation object 'plot.predictions':
  ‘plot.predictions’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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Unknown package ‘sparsebn’ in Rd xrefs
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Malformed Description field: should contain one or more complete sentences.
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Packages suggested but not available for checking: 'rhdf5', 'HDF5Array'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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GNU make is a SystemRequirements.
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Depends: includes the non-default packages:
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  'spatstat.model', 'spatstat.linnet', 'spatstat.data', 'spatstat',
  'rpanel', 'tcltk'
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selectively is preferable.
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  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
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selectively is preferable.
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selectively is preferable.
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  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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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
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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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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
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'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
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Package suggested but not available for checking: ‘mboost’
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
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checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    libs   3.3Mb
'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
Specified C++11: please drop specification unless essential
installed size is 16.7Mb
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    extdata   2.6Mb
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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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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    data   4.7Mb
Packages suggested but not available for checking: 'car', 'party'
'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  7.7Mb
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installed size is 50.2Mb
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    libs  48.3Mb
'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
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    data   5.3Mb
installed size is 12.3Mb
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    data   1.1Mb
    help   1.1Mb
    libs   9.9Mb
installed size is  8.7Mb
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Package suggested but not available for checking: ‘ecpc’
installed size is  5.6Mb
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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
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  25.5Mb
'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 99.2Mb
  sub-directories of 1Mb or more:
    libs  98.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    lsndata   2.3Mb
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘SSsimple.Snw’ using Sweave
Loading required package: mvtnorm
Error: processing vignette 'SSsimple.Snw' failed with diagnostics:
Running 'texi2dvi' on 'SSsimple.tex' failed.
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:
  ‘SSsimple.Snw’

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
'LazyData' is specified without a 'data' directory
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
installed size is 49.7Mb
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    libs  49.3Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    include  12.1Mb
    lib       2.5Mb
GNU make is a SystemRequirements.
installed size is 92.5Mb
  sub-directories of 1Mb or more:
    libs  91.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CVXR’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
Package suggested but not available for checking: ‘starsdata’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    1.7Mb
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Running examples in ‘Statamarkdown-Ex.R’ failed
The error most likely occurred in:

> ### Name: find_stata
> ### Title: A helper function that seeks to locate your Stata executable.
> ###   Ordinarily this is run automatically when 'Statamarkdown' is loaded.
> ### Aliases: find_stata
> 
> ### ** Examples
> 
> indoc <- '
+ # An R console example
+ ## In a first code chunk, set up with
+ ```{r}
+ library(Statamarkdown)
+ ```
+ 
+ ## Then mark Stata code chunks with
+ ```{stata}
+ sysuse auto, clear
+ generate gpm = 1/mpg
+ summarize price gpm
+ ```
+ '
> 
> if (!is.null(Statamarkdown::find_stata())) {
+   # To run this example, remove tempdir().
+   fmd <- file.path(tempdir(), "test.md")
+   fhtml <- file.path(tempdir(), "test.html")
+ 
+   knitr::knit(text=indoc, output=fmd)
+   rmarkdown::render(fmd, "html_document", fhtml)
+ }
No Stata executable found.
Warning in min(grep("[[:alnum:]]", y)) :
  no non-missing arguments to min; returning Inf
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is  6.9Mb
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    libs   6.2Mb
Specified C++11: please drop specification unless essential
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   5.1Mb
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
installed size is  5.0Mb
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    data   3.5Mb
installed size is  7.3Mb
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    extdata   2.4Mb
    libs      4.2Mb
installed size is  7.5Mb
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Package suggested 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: ‘tweedie’
Package unavailable to check Rd xrefs: ‘tweedie’
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'semPlot', 'FactoMineR', 'FactoInvestigate', 'factoextra'
installed size is  6.2Mb
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    shiny-apps   6.2Mb
installed size is  7.0Mb
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    libs   4.4Mb
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
installed size is 63.4Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘StMoMoVignette.Rnw’ using Sweave
Loading required package: gnm
Loading required package: forecast
Error: processing vignette 'StMoMoVignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'StMoMoVignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `ctable.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [caption = false]{subfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'StMoMoVignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.5Mb
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.5Mb
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 10.5Mb
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    libs  10.3Mb
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
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Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    doc   5.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
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    libs   5.0Mb
Package unavailable to check Rd xrefs: ‘HDoutliers’
installed size is 13.0Mb
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    doc    1.7Mb
    libs  10.0Mb
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
installed size is  5.5Mb
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    libs   4.1Mb
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.3Mb
Package suggested but not available for checking: ‘networkD3’
S3 methods shown with full name in documentation object 'size.penalize':
  ‘size.penalize’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'adegraphics', 'spdep'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'arm', 'caret', 'party'
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
Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
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    data   2.0Mb
    doc    3.3Mb
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘extraTrees’
Unknown package ‘extraTrees’ in Rd xrefs
Packages suggested but not available for checking:
  'arm', 'bartMachine', 'extraTrees', 'party', 'xgboost'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    2.2Mb
    libs   1.7Mb
installed size is 52.3Mb
  sub-directories of 1Mb or more:
    libs  51.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA', 'rstan'
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
installed size is 10.1Mb
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    R      2.0Mb
    data   2.3Mb
    doc    3.9Mb
Specified C++11: please drop specification unless essential
installed size is 12.1Mb
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    data  12.0Mb
Unknown package ‘survJamda’ in Rd xrefs
installed size is  6.0Mb
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    doc   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is 14.9Mb
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    libs  13.1Mb
'LazyData' is specified without a 'data' directory
installed size is 55.1Mb
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GNU make is a SystemRequirements.
installed size is  8.5Mb
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    help   1.0Mb
    libs   6.8Mb
'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 45.3Mb
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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
Package suggested but not available for checking: ‘swephRdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    libs   4.9Mb
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  44.0Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.5Mb
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    fonts   1.7Mb
    libs   19.7Mb
'LazyData' is specified without a 'data' directory
installed size is 23.3Mb
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    libs  23.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R         2.3Mb
    extdata   3.1Mb
Specified C++11: please drop specification unless essential
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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    doc   5.9Mb
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘psych’

Package which this enhances but not available for checking: ‘LSAmitR’
installed size is  7.4Mb
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    R      2.0Mb
    libs   4.5Mb
Package unavailable to check Rd xrefs: ‘psych’
S3 methods shown with full name in documentation object 'designMatrices':
  ‘print.designMatrices’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  13.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
'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.
Packages required but not available: 'microbiome', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dearseq’
Package unavailable to check Rd xrefs: ‘dearseq’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc  12.3Mb
installed size is  5.1Mb
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    tklibs   4.7Mb
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
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    libs   6.4Mb
Specified C++11: please drop specification unless essential
installed size is 13.9Mb
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    apps   2.3Mb
    libs   9.6Mb
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Package suggested but not available for checking: ‘R2wd’
checkRd: (-1) R2txt.Rd:164: Escaped LaTeX specials: \#
checkRd: (-1) bct.Rd:18: Escaped LaTeX specials: \^
checkRd: (-1) bct.Rd:19: Escaped LaTeX specials: \^
checkRd: (-1) ineq.Rd:10: Escaped LaTeX specials: \&
checkRd: (-1) put.points.demo.Rd:39: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:10: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:31: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is 17.9Mb
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    libs  15.2Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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    doc       3.7Mb
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    telemac   1.0Mb
Package suggested but not available for checking: ‘INLA’
installed size is 10.2Mb
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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  6.3Mb
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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 139-157 [unnamed-chunk-7] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
The engine "block2" is for R Markdown only
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
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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/terra.Rcheck/00install.out’ for details.
installed size is 31.7Mb
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Package suggested but not available for checking: ‘gurobi’
installed size is  8.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
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Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
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Specified C++11: please drop specification unless essential
installed size is  5.2Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Unknown package ‘textreadr’ in Rd xrefs
installed size is 21.6Mb
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installed size is 15.3Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘btable.Rnw’ using Sweave
Loading required package: textutils
Error: processing vignette 'btable.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'btable.tex' failed.
LaTeX errors:
! LaTeX Error: File `DejaVuSansMono.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'btable.Rnw'

SUMMARY: processing the following file failed:
  'btable.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  6.8Mb
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    libs   6.0Mb
'LazyData' is specified without a 'data' directory
installed size is 27.9Mb
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    libs  27.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
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    data   1.1Mb
    rda    7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'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
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggplot2’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lme4’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SingleR’
installed size is 46.7Mb
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    libs  45.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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    extdata   4.5Mb
installed size is 10.3Mb
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    libs   9.3Mb
installed size is  6.4Mb
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Package suggested but not available for checking: ‘rrelaxiv’
installed size is 55.7Mb
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    tiledb  38.1Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'org.Rn.eg.db', 'org.Mm.eg.db'
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is  6.9Mb
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    data   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is 63.0Mb
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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
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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    libs   4.5Mb
Specified C++14: please drop specification unless essential
installed size is  9.9Mb
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    libs   9.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
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installed size is 30.3Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: ‘Rpoppler’
'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  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Package required but not available: ‘EnhancedVolcano’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘ToolsForCoDa.Rnw’ using Sweave
Loading required package: mice

Attaching package: 'mice'

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

    filter

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

    cbind, rbind

Loading required package: Rsolnp
Loading required package: nnet
Loading required package: MASS
Loading required package: calibrate
Error: processing vignette 'ToolsForCoDa.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'ToolsForCoDa.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.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'ToolsForCoDa.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘stm’
Package unavailable to check Rd xrefs: ‘stm’
Package suggested but not available for checking: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
installed size is  7.4Mb
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    data   7.3Mb
installed size is 200.0Mb
  sub-directories of 1Mb or more:
    R          6.1Mb
    help       2.3Mb
    include    1.8Mb
    libs     189.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data  13.0Mb
'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   5.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ctmm’
Package unavailable to check Rd xrefs: ‘ctmm’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
Package suggested but not available for checking: ‘competitiontoolbox’
Package unavailable to check Rd xrefs: ‘competitiontoolbox’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
Specified C++11: please drop specification unless essential
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  46.5Mb
Package suggested but not available for checking: ‘tramnet’
Note: skipping ‘tramvs.Rnw’ due to unavailable dependencies: 'tramnet'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.6Mb
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    libs   7.5Mb
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
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    libs   5.5Mb
Package which this enhances but not available for checking: ‘fwelnet’
installed size is  5.1Mb
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    data   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR', 'Capr'
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Package required but not available: ‘phyloseq’

Package suggested but not available for checking: ‘adaptiveGPCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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’
installed size is  7.8Mb
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    doc    4.9Mb
    libs   2.2Mb
Package suggested but not available for checking: ‘Seurat’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  5.9Mb
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    datasets   1.6Mb
    doc        1.3Mb
    libs       1.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.2Mb
Package suggested but not available for checking: ‘brms’
Package unavailable to check Rd xrefs: ‘brms’
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    doc       1.3Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 114.4Mb
  sub-directories of 1Mb or more:
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    libs  109.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 39.5Mb
  sub-directories of 1Mb or more:
    libs  39.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'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/triptych.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
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
  sub-directories of 1Mb or more:
    libs   8.0Mb
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
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   8.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘rugarch’
Package unavailable to check Rd xrefs: ‘rugarch’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'tsibble-vctrs':
  ‘vec_ptype2.tbl_ts’ ‘vec_cast.tbl_ts’ ‘vec_cast.yearmonth’
  ‘vec_ptype2.yearmonth’ ‘vec_cast.yearquarter’
  ‘vec_ptype2.yearquarter’ ‘vec_cast.yearweek’ ‘vec_ptype2.yearweek’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'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 unavailable to check Rd xrefs: ‘twang’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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  9.3Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    ubinc   2.0Mb
installed size is 110.0Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     1.0Mb
    libs  106.8Mb
GNU make is a SystemRequirements.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
Specified C++11: please drop specification unless essential
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       22.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MortalityLaws’
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Unknown package ‘MortalityLaws’ in Rd xrefs
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.
'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 46.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.4Mb
    libs  41.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘adespatial’
'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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    data   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
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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S3 methods shown with full name in documentation object 'syntab':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
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See section 'Cross-references' in the 'Writing R Extensions' manual.
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--- re-building ‘introduction.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘introduction.Rmd’

--- re-building ‘shiny-example.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 61-63 [iframe] (shiny-example.Rmd)
Error: processing vignette 'shiny-example.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘shiny-example.Rmd’

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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S3 methods shown with full name in documentation object 'QIC.gee':
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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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Warning in initDict() :
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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.
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Unknown packages 'HI', 'MHadaptive' in Rd xrefs
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--- re-building 'adce.Rmd' using rmarkdown

Quitting from lines 135-146 [unnamed-chunk-8] (adce.Rmd)
Error: processing vignette 'adce.Rmd' failed with diagnostics:
argument "join_type" is missing, with no default
--- failed re-building 'adce.Rmd'

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

Quitting from lines 233-247 [unnamed-chunk-13] (adface.Rmd)
Error: processing vignette 'adface.Rmd' failed with diagnostics:
argument "join_type" is missing, with no default
--- failed re-building 'adface.Rmd'

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

Quitting from lines 551-562 [unnamed-chunk-19] (adis.Rmd)
Error: processing vignette 'adis.Rmd' failed with diagnostics:
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--- failed re-building 'adis.Rmd'

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

--- re-building 'adsl.Rmd' using rmarkdown
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SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
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No news entries found.
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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: \_ \_
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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 35.3Mb
  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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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:
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'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
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Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.4Mb
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    data   1.6Mb
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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
'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  5.2Mb
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Packages suggested but not available for checking:
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installed size is  5.3Mb
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 42.9Mb
  sub-directories of 1Mb or more:
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installed size is 14.3Mb
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checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Found the following significant warnings:
  rwin.c:28:8: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  rwin.c:251:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  rwin.c:283:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  rwin.c:291:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/asciicast.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'asteRiskData'
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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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
Unknown package 'snpar' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  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  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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    libs   3.5Mb
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  6.1Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
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installed size is  9.4Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Earlier versions
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
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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
GNU make is a SystemRequirements.
'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: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
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checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
installed size is  6.8Mb
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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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  5.1Mb
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Package suggested but not available for checking: 'INLA'
installed size is  6.8Mb
  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   5.5Mb
GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
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  7.5Mb
  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
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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    libs   2.2Mb
installed size is  5.8Mb
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installed size is  5.3Mb
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    doc    1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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    doc   3.9Mb
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:
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GNU make is a SystemRequirements.
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
installed size is 12.8Mb
  sub-directories of 1Mb or more:
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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  5.9Mb
  sub-directories of 1Mb or more:
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    extdata   3.3Mb
    libs      1.4Mb
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
S3 methods shown with full name in documentation object 'export.bce':
  'export.bce'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
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Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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  5.3Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.0Mb
'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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is 151.7Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
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checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
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Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'lavaan.survey'
Unknown package 'lavaan.survey' in Rd xrefs
Package suggested but not available for checking: 'ffbase'
Package suggested but not available for checking: 'INLA'
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'select.cfs':
  'select.cfs'

S3 methods shown with full name in documentation object 'select.fast.filter':
  'select.fast.filter'

S3 methods shown with full name in documentation object 'select.forward.Corr':
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S3 methods shown with full name in documentation object 'select.forward.wrapper':
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S3 methods shown with full name in documentation object 'select.inf.chi2':
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S3 methods shown with full name in documentation object 'select.inf.gain':
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S3 methods shown with full name in documentation object 'select.inf.symm':
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S3 methods shown with full name in documentation object 'select.process':
  'select.process'

S3 methods shown with full name in documentation object 'select.relief':
  'select.relief'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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    extdata   2.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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    doc    1.1Mb
    help   1.0Mb
    libs   1.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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    libs      1.2Mb
installed size is  6.1Mb
  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: \&
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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: \&
'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
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  7.7Mb
  sub-directories of 1Mb or more:
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    libs       4.9Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
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    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
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
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is 40.8Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      29.8Mb
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.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
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Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
S3 methods shown with full name in documentation object 'subset.int':
  'subset.int'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'cmdstanr'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: 'glmmADMB'
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 11.6Mb
  sub-directories of 1Mb or more:
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    lib     4.5Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/bsts.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'gvcm.cat'
Specified C++11: please drop specification unless essential
Unknown package 'gvcm.cat' in Rd xrefs
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:
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    extdata   3.4Mb
'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  5.0Mb
  sub-directories of 1Mb or more:
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Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
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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
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 38.0Mb
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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 12.2Mb
  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
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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Unexported objects imported by ':::' calls:
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  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major refactoring of the code
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.7Mb
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'select.cglasso':
  'select.cglasso'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'internals':
  'max.rss'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'darts'
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Package suggested but not available for checking: 'countreg'
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Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.5Mb
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installed size is 18.0Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'entab'
'LazyData' is specified without a 'data' directory
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installed size is  8.0Mb
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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
installed size is  6.5Mb
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Package suggested but not available for checking: 'userfriendlyscience'
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'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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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
'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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'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
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
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    doc    1.9Mb
installed size is  5.5Mb
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    doc   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
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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
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
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Package suggested but not available for checking: 'tobit1'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg19'
installed size is  5.2Mb
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Package suggested but not available for checking: 'PopGenome'
Package suggested but not available for checking: 'disttree'
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checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
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Package which this enhances but not available for checking: 'rkward'
Package which this enhances but not available for checking: 'rkward'
Package suggested but not available for checking: 'userfriendlyscience'
'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  5.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
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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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
'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'
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
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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
'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
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    vignette_data   2.6Mb
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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installed size is  7.2Mb
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checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
installed size is  5.1Mb
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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  5.9Mb
  sub-directories of 1Mb or more:
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/coursekata.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
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    extdata   2.6Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'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:
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/crc32c.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer3'
installed size is  6.5Mb
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Package suggested but not available for checking: 'EnsDb.Hsapiens.v86'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
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    doc    1.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'internals':
  'qr.gs'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
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    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  7.9Mb
  sub-directories of 1Mb or more:
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    libs   5.8Mb
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.
'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'
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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
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.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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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
Package which this enhances but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Package suggested but not available for checking: 'SASxport'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
S3 methods shown with full name in documentation object 'dbglm-inl':
  'dbglm.iteration'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'BRugs'
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'Rdonlp2'
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checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
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'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  6.8Mb
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Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
'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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    htmlwidgets   3.6Mb
GNU make is a SystemRequirements.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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S3 methods shown with full name in documentation object 'add.joint.mean.many':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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GNU make is a SystemRequirements.
S3 methods shown with full name in documentation object 'addDrug.Lexis':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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S3 methods shown with full name in documentation object 'summary.error_interval':
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S3 methods shown with full name in documentation object 'summary.measure':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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The \usage entries for S3 methods should use the \method markup and not
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See chapter 'Writing R documentation files' in the 'Writing R
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* used C compiler: 'gcc.exe (GCC) 12.3.0'
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    images   3.1Mb
    libs     1.3Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'coxKM'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    Rcgi      3.0Mb
    cgi-bin   2.8Mb
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Undefined global functions or variables:
  init run
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'NNLM'
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
    libs   1.6Mb
Unexported object imported by a ':::' call: 'fdapace:::interp2lin'
  See the note in ?`:::` about the use of this operator.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    extdata   2.8Mb
    libs      1.2Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'MicrobeDS'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    3.0Mb
    help   1.1Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R         4.7Mb
    doc       2.1Mb
    extdata   2.1Mb
'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  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'diveRsity'
Unknown package 'diveRsity' in Rd xrefs
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    lib    3.0Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fivethirtyeightdata'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    3.6Mb
    libs   1.6Mb
'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  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) cclust.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) randIndex.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:28: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  22.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    9.1Mb
    libs   1.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'fmsb-Ex.R' failed
The error most likely occurred in:

> ### Name: WhipplesIndex
> ### Title: Whipple's Index
> ### Aliases: WhipplesIndex
> 
> ### ** Examples
> 
>  WhipplesIndex(Jpop$M2000)
$WI
[1] 99.09955

$JUDGE
[1] "highly accurate"

>  India <- read.delim("https://minato.sip21c.org/ldaR/India2011census.txt")
Warning in file(file, "rt") :
  URL 'https://minato.sip21c.org/ldaR/India2011census.txt': status was 'SSL connect error'
Error in file(file, "rt") : 
  cannot open the connection to 'https://minato.sip21c.org/ldaR/India2011census.txt'
Calls: read.delim -> read.table -> file
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RandomFields'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   3.4Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.8Mb
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  Warning: replacing previous import 'lwgeom::st_perimeter' by 'sf::st_perimeter' when loading 'fsr'
See 'd:/Rcompile/CRANpkg/local/4.3/fsr.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
S3 methods shown with full name in documentation object 'plot.funData':
  'plot.funData'

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   4.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Specified C++14: please drop specification unless essential
installed size is 46.2Mb
  sub-directories of 1Mb or more:
    doc   44.3Mb
    libs   1.2Mb
':::' call which should be '::': 'graphics:::grid'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'tools:::.Rd_get_argument_names' 'tools:::RdTags' 'tools:::fetchRdDB'
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'paleofire'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 105.1Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
    libs     87.8Mb
    proj      8.2Mb
installed size is 104.6Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     3.0Mb
    libs    89.9Mb
    proj     8.3Mb
installed size is 101.9Mb
  sub-directories of 1Mb or more:
    gdal   3.0Mb
    libs  88.3Mb
    proj   8.3Mb
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
'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:
    doc       1.5Mb
    extdata   3.2Mb
    libs      1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'genderdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.4Mb
'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:
    doc       2.1Mb
    extdata   3.5Mb
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
  sub-directories of 1Mb or more:
    R         9.6Mb
    extdata   2.5Mb
    help      2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'RandomFields'

Package which this enhances but not available for checking: 'INLA'
Unknown package 'RandomFields' in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
help_secondary: possible error in sec_axis(transform = help$reverse,
  ...): unused argument (transform = help$reverse)
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   7.0Mb
'LazyData' is specified without a 'data' directory
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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  5.2Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   1.9Mb
'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
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.4Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
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
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    Giac  17.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   2.5Mb
'LazyData' is specified without a 'data' directory
Unknown package 'IC2' in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'mlr3proba'
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.0Mb
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc             1.4Mb
    libs            4.4Mb
    test_data       2.2Mb
    vignette_data   1.2Mb
'LazyData' is specified without a 'data' directory
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Malformed Description field: should contain one or more complete sentences.
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installed size is  6.5Mb
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Unknown package 'gvcm.cat' in Rd xrefs
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installed size is  5.5Mb
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installed size is  5.3Mb
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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'
installed size is  5.1Mb
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    doc   2.7Mb
GNU make is a SystemRequirements.
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S3 methods shown with full name in documentation object 'groc.fit':
  'groc.fit'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  6.0Mb
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installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
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installed size is 250.1Mb
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    java  247.1Mb
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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:
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  '.ga.weight'
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Error(s) in re-building vignettes:
--- re-building 'harmonicmeanp.Rmd' using rmarkdown

Quitting from lines 389-402 [fiddler] (harmonicmeanp.Rmd)
Error: processing vignette 'harmonicmeanp.Rmd' failed with diagnostics:
need finite 'xlim' values
--- failed re-building 'harmonicmeanp.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
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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 11.3Mb
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GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.1Mb
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GNU make is a SystemRequirements.
installed size is  5.1Mb
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installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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'LazyData' is specified without a 'data' directory
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installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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    data   1.5Mb
    doc    3.7Mb
installed size is  6.2Mb
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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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    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
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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S3 methods shown with full name in documentation object 'defunct':
  'anova.mean' 'print.glht.mmc.multicomp' 'coef.arima.HH' 'glht.mmc'
  'plot.odds.ratio' 'persp.plane' 'persp.floor' 'persp.back.wall.x'
  'persp.back.wall.y' 'persp.setup' 'plot.hov' 'plot.hov.bf'
  'plot.matchMMC' 'seqplot.forecast'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'colorfulVennPlot'
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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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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'trackr'
Package which this enhances but not available for checking: 'HadoopStreaming'
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installed size is  5.1Mb
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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
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'LazyData' is specified without a 'data' directory
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installed size is 14.9Mb
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Package suggested but not available for checking: 'glmmADMB'
installed size is  5.2Mb
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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
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'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
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installed size is  8.4Mb
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checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
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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: 'hurricaneexposuredata'
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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  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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installed size is  6.4Mb
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checkRd: (-1) palettes.Rd:25: 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
Package suggested but not available for checking: 'SparkR'
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installed size is  6.1Mb
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    data   6.1Mb
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Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
'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
Package suggested but not available for checking: 'icd'
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
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checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'internals':
  'plot.page'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'IFCdata'
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installed size is 10.8Mb
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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
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installed size is 11.4Mb
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  sub-directories of 1Mb or more:
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    doc       5.2Mb
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installed size is 21.6Mb
  sub-directories of 1Mb or more:
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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: 'accdata'
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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
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Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
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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'
installed size is  5.0Mb
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Package suggested but not available for checking: 'cmdstanr'
Malformed Title field: should not end in a period.
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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
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
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    doc   9.9Mb
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Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
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'LazyData' is specified without a 'data' directory
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
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
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S3 methods shown with full name in documentation object 'print.Item':
  'print.Item'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
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installed size is  8.1Mb
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    doc    2.3Mb
    libs   3.0Mb
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
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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'
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installed size is 13.2Mb
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    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'.
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    pre-release juicr (2017 - 2021)
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S3 methods shown with full name in documentation object 'bw.abram.temp':
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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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S3 methods shown with full name in documentation object 'unlist.constr':
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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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    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
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S3 methods shown with full name in documentation object 'BIC.threshold.ggm':
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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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Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(magclass)
  > 
  > test_check("magclass")
  Error in R_nc4_open: NetCDF: Unknown file format
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 726 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • quitte cannot be loaded (2): 'test-as.magpie.R:22:3', 'test-as.magpie.R:63:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-readwritemagpie.R:87:3'): handling of spatial data works ───────
  Error in `ncdf4::nc_open(filename, readunlim = FALSE, suppress_dimvals = TRUE)`: Error in nc_open trying to open file D:\temp\RtmpeyTTdx\test.nc (return_on_error= FALSE )
  Backtrace:
       ▆
    1. ├─testthat::expect_no_warning(write.magpie(m10, file.path(td, "test.nc"))) at test-readwritemagpie.R:87:3
    2. │ └─testthat:::expect_no_(...)
    3. │   └─testthat:::quasi_capture(enquo(object), NULL, capture)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─rlang::try_fetch(...)
    6. │     │   └─base::withCallingHandlers(...)
    7. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    8. └─magclass::write.magpie(m10, file.path(td, "test.nc"))
    9.   ├─magclass:::suppressSpecificWarnings(...)
   10.   │ └─base::withCallingHandlers(...)
   11.   ├─raster::writeRaster(...)
   12.   └─raster::writeRaster(...)
   13.     └─raster (local) .local(x, filename, ...)
   14.       └─raster:::.stopWriteCDF(b)
   15.         ├─raster::brick(x@file@name)
   16.         └─raster::brick(x@file@name)
   17.           └─raster:::.rasterObjectFromFile(...)
   18.             └─raster:::.rasterObjectFromCDF(...)
   19.               └─ncdf4::nc_open(filename, readunlim = FALSE, suppress_dimvals = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 726 ]
  Error: Test failures
  Execution halted
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    Bug Fixes
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.7Mb
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Package suggested but not available for checking: 'gurobi'
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Running examples in 'matric-Ex.R' failed
The error most likely occurred in:

> ### Name: sim_read
> ### Title: Read similarity matrix.
> ### Aliases: sim_read
> 
> ### ** Examples
> 
> suppressMessages(suppressWarnings(library(magrittr)))
> population <- tibble::tibble(
+   Metadata_group = sample(c("a", "b"), 4, replace = TRUE),
+   x = rnorm(4),
+   y = x + rnorm(4) / 100,
+   z = y + rnorm(4) / 1000
+ )
> tmpdir <- tempdir()
> tmpfile_prefix <- file.path(tmpdir, "test")
> tmpfile_parquet <- file.path(tmpdir, "test.pqrquet")
> sim_df <- sim_calculate(population, method = "pearson")
> sim_df %>% sim_write(tmpfile_prefix, file_format = "csv")
INFO [2024-01-03 13:41:33] Creating D:\temp\RtmpeYuNOi/test ...
INFO [2024-01-03 13:41:33] Writing D:\temp\RtmpeYuNOi/test/test.csv ...
INFO [2024-01-03 13:41:33] Writing D:\temp\RtmpeYuNOi/test/test_metadata.csv ...
INFO [2024-01-03 13:41:33] Writing D:\temp\RtmpeYuNOi/test/test_metadata.json ...
NULL
> sim_df_csv <- sim_read(tmpfile_prefix, file_format = "csv")
INFO [2024-01-03 13:41:33] Reading D:\temp\RtmpeYuNOi/test/test.csv ...
INFO [2024-01-03 13:41:33] Reading D:\temp\RtmpeYuNOi/test/test_metadata.csv ...
INFO [2024-01-03 13:41:33] Reading D:\temp\RtmpeYuNOi/test/test_metadata.json ...
> sim_df %>% sim_write(tmpfile_parquet)
INFO [2024-01-03 13:41:34] Writing D:\temp\RtmpeYuNOi/test.pqrquet ...
NULL
> sim_df_parquet1 <- sim_read(tmpfile_parquet)
> sim_df %>% arrow::write_parquet(tmpfile_parquet)
Error: IOError: Failed to open local file 'D:/temp/RtmpeYuNOi/test.pqrquet'. Detail: [Windows error 1224] Der Vorgang ist bei einer Datei mit einem geöffneten Bereich, der einem Benutzer zugeordnet ist, nicht anwendbar.
Execution halted
Running 'testthat.R' [103s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(matric)
  > 
  > test_check("matric")
  
  Attaching package: 'purrr'
  
  The following object is masked from 'package:testthat':
  
      is_null
  
  [ FAIL 1 | WARN 66 | SKIP 0 | PASS 93 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-sim_read-write.R:100:3'): `sim_read` works ─────────────────────
  Error: IOError: Failed to open local file 'D:/temp/RtmpC4t00F/test.parquet'. Detail: [Windows error 1224] Der Vorgang ist bei einer Datei mit einem geöffneten Bereich, der einem Benutzer zugeordnet ist, nicht anwendbar.
  
  Backtrace:
      ▆
   1. ├─sim_df %>% arrow::write_parquet(tmp_parquet_file) at test-sim_read-write.R:100:3
   2. └─arrow::write_parquet(., tmp_parquet_file)
   3.   └─arrow:::make_output_stream(sink)
   4.     └─FileOutputStream$create(x)
   5.       └─arrow:::io___FileOutputStream__Open(clean_path_abs(path))
  
  [ FAIL 1 | WARN 66 | SKIP 0 | PASS 93 ]
  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
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: 'doMC'
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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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installed size is  5.5Mb
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    libs   1.5Mb
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
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installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
Found the following significant warnings:
  datablock.h:124:42: warning: pointer used after 'void operator delete(void*)' [-Wuse-after-free]
See 'd:/Rcompile/CRANpkg/local/4.3/MCMCpack.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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installed size is  7.4Mb
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Package suggested but not available for checking: 'cmdstanr'
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial version.
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Package suggested but not available for checking: 'RGtk2'
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installed size is  7.5Mb
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    doc       1.9Mb
    extdata   5.2Mb
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Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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Package suggested but not available for checking: 'MethylCapSig'
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Package suggested but not available for checking: 'cmdstanr'
installed size is  5.4Mb
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    libs   4.0Mb
GNU make is a SystemRequirements.
'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
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
installed size is  6.0Mb
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    extdata   3.4Mb
    libs      1.2Mb
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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    libs   6.9Mb
'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  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    help   2.2Mb
installed size is  5.2Mb
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    data   4.2Mb
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installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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installed size is  5.9Mb
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    doc    2.3Mb
    help   2.0Mb
    libs   1.2Mb
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installed size is  8.7Mb
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    R      1.7Mb
    doc    2.8Mb
    libs   2.3Mb
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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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'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: 'structSSI'
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S3 methods shown with full name in documentation object 'complete.miceadds':
  'complete.mids.nmi' 'complete.mids.1chain'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'microcontax.data'
Package unavailable to check Rd xrefs: 'microcontax.data'
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installed size is  8.7Mb
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    doc    5.5Mb
    lib    1.2Mb
    libs   1.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Found the following significant warnings:
  subfunc.cpp:322:20: warning: 'arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.3/minimaxdesign.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
':::' call which should be '::': 'parallel:::detectCores'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'BRugs'
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  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    include   9.7Mb
    libs     16.9Mb
Error(s) in re-building vignettes:
--- re-building 'Simulations.Rmd' using rmarkdown

Quitting from lines 543-708 [SimulationsAnimintClassification] (Simulations.Rmd)
Error: processing vignette 'Simulations.Rmd' failed with diagnostics:
Passed a vector of type 'NULL'. Needs to be type 'character'.
--- failed re-building 'Simulations.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Problems with news in 'NEWS.md':
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'LazyData' is specified without a 'data' directory
installed size is 13.7Mb
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    libs  13.2Mb
Problems with news in 'NEWS.md':
No news entries found.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/MM2S.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
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    images   1.1Mb
    shiny   14.5Mb
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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
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No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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    libs   4.4Mb
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No news entries found.
Package suggested but not available for checking: 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Packages suggested but not available for checking:
  'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'BSgenome.Hsapiens.UCSC.hg19'
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'LazyData' is specified without a 'data' directory
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installed size is 14.7Mb
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    data   2.0Mb
    libs   1.5Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    data   4.5Mb
    libs   1.2Mb
installed size is  5.1Mb
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    libs   4.7Mb
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installed size is  6.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'pca.plot.wrap':
  'lda.plot.wrap.1'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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No news entries found.
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'LazyData' is specified without a 'data' directory
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installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
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installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   7.8Mb
GNU make is a SystemRequirements.
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    doc    2.6Mb
    help   2.2Mb
    libs   1.1Mb
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installed size is  5.0Mb
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    doc   4.3Mb
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Package unavailable to check Rd xrefs: 'rTubeDB'
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installed size is 16.2Mb
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Problems with news in 'NEWS.md':
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    Version (2018-01-22)
    Version  (2017-08-22)
    Version
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GNU make is a SystemRequirements.
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installed size is 15.7Mb
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Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
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GNU make is a SystemRequirements.
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':::' call which should be '::': 'lhs:::maximinLHS'
  See the note in ?`:::` about the use of this operator.
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installed size is  7.9Mb
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Package which this enhances but not available for checking: 'jpndistrict'
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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No news entries found.
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Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                   old_size new_size compress
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installed size is 10.3Mb
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Running examples in 'oldbailey-Ex.R' failed
The error most likely occurred in:

> ### Name: find_trials
> ### Title: Find Old Bailey Trials
> ### Aliases: find_trials
> 
> ### ** Examples
> 
> # Return a dataframe with 5 trials.
> trials <- find_trials(n_results = 5)
Error: lexical error: invalid char in json text.
                                       <!doctype html><html lang="en">
                     (right here) ------^
Execution halted
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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
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'unix'
GNU make is a SystemRequirements.
installed size is 30.3Mb
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S3 methods shown with full name in documentation object 'unary_ops':
  'log10.ProcessNode' 'log10.ProcessGraphParameter'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.1Mb
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installed size is  5.1Mb
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installed size is 16.1Mb
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GNU make is a SystemRequirements.
installed size is  7.2Mb
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Package suggested but not available for checking: 'openNLPmodels.en'
Error(s) in re-building vignettes:
--- re-building 'osem-history.Rmd' using rmarkdown
--- finished re-building 'osem-history.Rmd'

--- re-building 'osem-history_revised.Rmd' using rmarkdown
--- finished re-building 'osem-history_revised.Rmd'

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

Quitting from lines 147-148 [unnamed-chunk-11] (osem-intro.Rmd)
Error: processing vignette 'osem-intro.Rmd' failed with diagnostics:
sf_column_name %in% all_sfc_names is not TRUE
--- failed re-building 'osem-intro.Rmd'

--- re-building 'osem-serialization.Rmd' using rmarkdown
--- finished re-building 'osem-serialization.Rmd'

SUMMARY: processing the following file failed:
  'osem-intro.Rmd'

Error: Vignette re-building failed.
Execution halted
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installed size is  5.3Mb
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installed size is  5.1Mb
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Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'gurobi'
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Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: 'gurobi'
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Package suggested but not available for checking: 'gurobi'
Problems with news in 'NEWS.md':
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Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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installed size is  5.2Mb
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Package suggested but not available for checking: 'Rcplex'
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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
'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
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Package which this enhances but not available for checking: 'CorShrink'
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S3 methods shown with full name in documentation object 'pamr-internal':
  'print.nsc' 'print.nsccv'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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S3 methods shown with full name in documentation object 'vec_cast.partial_time':
  'vec_cast.partial_time'

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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GNU make is a SystemRequirements.
installed size is  8.1Mb
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    R      6.1Mb
    help   1.9Mb
installed size is  6.0Mb
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S3 methods shown with full name in documentation object 'ped':
  'ped.markerNames'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/pbdSLAP.Rcheck/00install.out' for details.
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Malformed Description field: should contain one or more complete sentences.
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Found the following significant warnings:
  d:/rtools43/x86_64-w64-mingw32.static.posix/include/coin/Clp_C_Interface.h:68:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/pcaL1.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
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GNU make is a SystemRequirements.
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S3 methods shown with full name in documentation object 'format.relation':
  'format.relation'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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Problems with news in 'NEWS.md':
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    Fixed issues
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S3 methods shown with full name in documentation object 'qr.solve_exact':
  'qr.solve_exact'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
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installed size is  6.8Mb
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installed size is 12.1Mb
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    data   4.6Mb
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    doc    1.7Mb
    libs   1.0Mb
installed size is  5.5Mb
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    libs      1.3Mb
installed size is  7.0Mb
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GNU make is a SystemRequirements.
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Missing link or links in documentation object 'pop.predict.Rd':
  'rrBLUP'

Missing link or links in documentation object 'x.val.Rd':
  'rrBLUP'

See section 'Cross-references' in the 'Writing R Extensions' manual.
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installed size is  6.6Mb
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installed size is 12.1Mb
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installed size is 13.3Mb
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    data      1.1Mb
    extdata  11.6Mb
Package which this enhances but not available for checking: 'ffbase'
Unknown package 'ffbase' in Rd xrefs
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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
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installed size is 10.0Mb
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installed size is  5.5Mb
  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
Package suggested but not available for checking: 'INLA'
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Packages suggested but not available for checking:
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installed size is  6.1Mb
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Packages suggested but not available for checking:
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installed size is  9.5Mb
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    doc    4.7Mb
    libs   1.6Mb
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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
installed size is 11.5Mb
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    htmlwidgets   2.5Mb
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installed size is 15.0Mb
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installed size is 23.5Mb
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    proj   8.3Mb
installed size is  8.2Mb
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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 10.5Mb
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installed size is  6.2Mb
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Found the following significant warnings:
  arch/windows/process_handles.h:100:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  arch/windows/process_handles.c:23:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/ps.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
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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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    examples   2.6Mb
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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
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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  5.6Mb
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    staticdocs   3.3Mb
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'LazyData' is specified without a 'data' directory
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S3 methods shown with full name in documentation object 'internals':
  'format.perc'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 26.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'internals':
  'plot.piqr2'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'internals':
  'predict.iqrL.internal'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
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installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    doc    4.4Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      2.6Mb
installed size is  5.0Mb
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    extdata   3.0Mb
    libs      1.0Mb
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installed size is 10.2Mb
  sub-directories of 1Mb or more:
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    contrib   3.7Mb
    doc       2.9Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    libs   1.4Mb
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'fastshp'
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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  7.1Mb
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    doc         3.7Mb
    shiny_app   1.4Mb
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'ReGenesees'
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installed size is  5.1Mb
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Package suggested but not available for checking: 'RDCOMClient'
'library' or 'require' call to 'RDCOMClient' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'BRugs'
installed size is 11.5Mb
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installed size is  7.3Mb
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    htmlwidgets   1.8Mb
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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
installed size is 10.6Mb
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    doc    6.7Mb
    libs   1.1Mb
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installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs          2.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
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installed size is 11.6Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   6.8Mb
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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
'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
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'gurobi'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   1.4Mb
'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   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.5Mb
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    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
installed size is  6.5Mb
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    data   3.9Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   1.2Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'export.default':
  'export.default'

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'rrelaxiv'
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installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
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installed size is 24.3Mb
  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
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  8.8Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   4.5Mb
    po    2.4Mb
Package suggested but not available for checking: 'conics'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rcplex.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
    libs      1.2Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    include  46.4Mb
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.2Mb
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.1Mb
GNU make is a SystemRequirements.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include        2.0Mb
    jsonexamples   3.8Mb
    libs           2.0Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'devAll'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'DIDmultiplegt'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.5Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 10.3Mb
  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  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.3Mb
'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: 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.4Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:42: Escaped LaTeX specials: \$
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) 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  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs      1.7Mb
    models    1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    data  13.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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  8.3Mb
  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  9.3Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs    2.6Mb
'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
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
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    lib    3.3Mb
    libs   4.1Mb
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Rinit.c:170:24: warning: pointer targets in passing argument 2 of 'Re_ReadConsole' differ in signedness [-Wpointer-sign]
  Rinit.c:251:21: warning: assignment to 'int (*)(const char *, unsigned char *, int,  int)' from incompatible pointer type 'int (*)(const char *, char *, int,  int)' [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.3/rJava.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Found the following possibly unsafe calls:
File 'rJava/R/import.R':
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File 'rJava/R/jinit.R':
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  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  6.1Mb
  sub-directories of 1Mb or more:
    include   3.1Mb
    libs      2.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  45.7Mb
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    extdata  23.8Mb
'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  5.2Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
GNU make is a SystemRequirements.
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    hdf5     16.0Mb
    include   6.5Mb
    lib       2.6Mb
    libs      8.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs       1.0Mb
    minizinc   2.3Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
Package suggested but not available for checking: 'rnaturalearthhires'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
'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  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\emmintrin.h:134:24: warning: array subscript '__m128d_u[0]' is partly outside array bounds of 'Eigen::internal::plain_matrix_type<Eigen::Product<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>, Eigen::Transpose<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false> >, 0>, Eigen::Dense>::type [1]' {aka 'Eigen::Matrix<double, 1, 1, 0, 1, 1> [1]'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.3/RobustGaSP.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              1.3Mb
    simulationStudy   1.6Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'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  5.4Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/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  5.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   1.5Mb
'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  6.7Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs   1.5Mb
Package suggested but not available for checking: 'RandomFields'
GNU make is a SystemRequirements.
Found the following significant warnings:
  phylopars_rcpp.cpp:125:26: warning: 'void arma::set_cerr_stream(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  phylopars_rcpp.cpp:144:26: warning: 'void arma::set_cerr_stream(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  phylopars_rcpp.cpp:179:26: warning: 'void arma::set_cerr_stream(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.3/Rphylopars.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
'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  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
'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  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
GNU make is a SystemRequirements.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    4.7Mb
    libs  11.6Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib    2.1Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
Specified C++11: please drop specification unless essential
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/rswipl.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.4Mb
    help   2.3Mb
'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:
    rmarkdown  11.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object 'printHTML.trackInfo':
  'printHTML.trackInfo'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs      5.2Mb
Problems with news in 'NEWS.md':
No news entries found.
S3 methods shown with full name in documentation object 'matmult':
  '%*%.rv'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rWCVPdata'
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
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  5.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   2.6Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'unix'
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
matrixOps:
  function(x, y)
matrixOps.S7_object:
  function(e1, e2)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  13.5Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   1.3Mb
Package suggested but not available for checking: 'networkTomography'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'FitARMA'
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
'library' or 'require' call to 'progress' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'sceasy', 'SeuratDisk', 'SeuratWrappers'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'plot':
  'plot.discretization'

S3 methods shown with full name in documentation object 'predict':
  'predict.discretization' 'predict.reject_infered'

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
installed size is 19.1Mb
  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  5.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   2.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spgrass6'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    www  33.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs     3.3Mb
    models   1.6Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BPCells'
Packages suggested but not available for checking: 'BPCells', 'presto'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
--- re-building 'sfdct.Rmd' using rmarkdown

Quitting from lines 94-98 [unnamed-chunk-3] (sfdct.Rmd)
Error: processing vignette 'sfdct.Rmd' failed with diagnostics:
key.width too small, try key.width = lcm(4.27)
--- failed re-building 'sfdct.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 106.4Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    gdal     3.0Mb
    libs    88.8Mb
    proj     8.3Mb
    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
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   6.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.8Mb
'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  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.4Mb
'LazyData' is specified without a 'data' directory
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 20.4Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    www   9.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg19'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    help      1.7Mb
    libs      1.0Mb
'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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'fg_step_tab_pp'
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
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  5.8Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   1.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Unknown package 'InformationValue' in Rd xrefs
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
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checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  glog.cpp:151:10: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  glog.cpp:253:10: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  glog.cpp:286:15: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  glog.cpp:320:13: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  glog.cpp:369:10: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.3/smog.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'doMC'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.3Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'lseq'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     3.3Mb
    doc   1.1Mb
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.solveEnv'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.3Mb
    libs   1.7Mb
S3 methods shown with full name in documentation object 'plot.predictions':
  'plot.predictions'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NLMR'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R   4.7Mb
Package suggested but not available for checking: 'NLMR'
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    libs   1.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    java   3.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Unknown package 'sparsebn' in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  grad_est.cpp:33:19: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  grad_est.cpp:98:19: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  grad_est.cpp:116:10: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  grad_est.cpp:133:19: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  grad_est.cpp:160:20: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  hmc4sfa.cpp:45:14: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  test_gamma_pois.cpp:30:13: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.3/SparseFactorAnalysis.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.1Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat.data', 'spatstat',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
    etc   1.4Mb
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  6.2Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Feature Changes
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs      1.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  13.8Mb
'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  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: replacing previous import 'lwgeom::st_perimeter' by 'sf::st_perimeter' when loading 'stampr'
See 'd:/Rcompile/CRANpkg/local/4.3/stampr.Rcheck/00install.out' for details.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    include  11.3Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    To do
Package suggested but not available for checking: 'starsdata'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    1.7Mb
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.4Mb
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
Running examples in 'statGraph-Ex.R' failed
The error most likely occurred in:

> ### Name: tang.test
> ### Title: Tang hypothesis testing for random graphs.
> ### Aliases: tang.test
> 
> ### ** Examples
> 
> set.seed(42)
> 
> ## test under H0
> lpvs <- matrix(rnorm(200), 20, 10)
> lpvs <- apply(lpvs, 2, function(x) { return (abs(x)/sqrt(sum(x^2))) })
> G1 <- igraph::sample_dot_product(lpvs)
> G2 <- igraph::sample_dot_product(lpvs)
> D1 <- tang.test(G1, G2, 5)
Error in defaults$maxiter <- .Machine$integer.max : 
  object of type 'closure' is not subsettable
Calls: tang.test -> t.embed.graph
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: 'networksis'
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.1Mb
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
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
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.
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'STRaitRazoR'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'size.penalize':
  'size.penalize'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'extraTrees'
Unknown package 'extraTrees' in Rd xrefs
Package suggested but not available for checking: 'extraTrees'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
surfaceSimulate : phytransform: no visible global function definition
  for 'rescale'
Undefined global functions or variables:
  rescale
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.2Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
Package suggested but not available for checking: 'distr6'
Unknown package 'distr6' in Rd xrefs
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.9Mb
Specified C++11: please drop specification unless essential
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Unknown package 'survJamda' in Rd xrefs
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'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
Package suggested but not available for checking: 'swephRdata'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/symengine.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'unix'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
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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
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'designMatrices':
  'print.designMatrices'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tashudata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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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 13.4Mb
  sub-directories of 1Mb or more:
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Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) R2txt.Rd:164: Escaped LaTeX specials: \#
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checkRd: (-1) bct.Rd:19: Escaped LaTeX specials: \^
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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    libs      1.1Mb
    telemac   1.0Mb
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    4.5Mb
    help   2.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 106.5Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    gdal   3.0Mb
    libs  91.6Mb
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installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       8.1Mb
    tessdata  14.0Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
installed size is  5.2Mb
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    data   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Unknown package 'textreadr' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'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
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    data   3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   4.5Mb
Package suggested but not available for checking: 'rrelaxiv'
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
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checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
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No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:131:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:334:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:453:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:471:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:496:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:497:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:509:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:522:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:1053:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:93:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:94:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/tkrplot.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.9Mb
  sub-directories of 1Mb or more:
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    include    3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data-tables   1.4Mb
    doc           1.9Mb
    help          1.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'corpus.JSS.papers'
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    R         5.6Mb
    help      1.6Mb
    include   1.8Mb
    libs     17.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'toscaData'
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taxidata'
Specified C++11: please drop specification unless essential
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  13.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'fwelnet', 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR', 'Capr'
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'TreeDistData'
installed size is  6.8Mb
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    doc    5.0Mb
    libs   1.2Mb
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Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    doc       1.3Mb
    extdata  14.8Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.4Mb
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
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'log2console'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
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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
S3 methods shown with full name in documentation object 'tsibble-vctrs':
  'vec_ptype2.tbl_ts' 'vec_cast.tbl_ts' 'vec_cast.yearmonth'
  'vec_ptype2.yearmonth' 'vec_cast.yearquarter'
  'vec_ptype2.yearquarter' 'vec_cast.yearweek' 'vec_ptype2.yearweek'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'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
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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  9.3Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    ubinc   2.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.0Mb
    libs   4.4Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.6Mb
'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:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.4Mb
    libs  14.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'USA.state.boundaries.data'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
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: \_ \_ \_
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checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
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installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   6.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  randutils.c:60:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  22.0Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 103.4Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    gdal      3.0Mb
    libs     88.0Mb
    proj      8.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
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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
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs     10.5Mb
GNU make is a SystemRequirements.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'syntab':
  'print.syntab'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
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checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
'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:
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    help   3.0Mb
Missing link or links in documentation object 'profilevglm.Rd':
  '[stats]{plot.profile}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
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    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
installed size is 21.8Mb
  sub-directories of 1Mb or more:
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    libs     19.9Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.5Mb